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1. Bilateral symmetry appears to be universally advantageous for complex organisms. There are very few examples of non-bilateral life on Earth that is more advanced than a starfish; so, assume this to be common elsewhere too. It also means that all of the below assertions should assume an even number of arms, legs, etc. Though throwing in 1 or 2 radially symmetrical races, or bilateral races with a central appendage creating an odd number could be believable too.
2. If you live in an aquatic environment, you can be smart, but never develop fire which means you will never develop chemistry, metallurgy, or ceramics or any of the other things that helped humans get out of the stone age. This means that nearly all of your aliens should be terrestrial or amphibious, and come from an oxygen rich planet.
3. If you don't have something like fingers, then you will be very dexterity limited in your tool use. Again, this caps you at a very primitive state. So, all of your aliens should have something like hands with multiple fingers. Something more tentacle like works too, but don't give them suckers because those require an aquatic environment to form a good seal.
4. If you have less than 2 arms, you will have a hard time manipulating objects against each-other and if you have more than 2 primary arms, then your arms will be strength limited compared to your size. So, most of your aliens should have 2 main arms, plus maybe 2-4 smaller arms or arms that second as feet. More than 6 arms with no fingers might happen too, where the arms work together for grasping, but expect that to be more rare since it wastes a lot more body mass on the extra appendages compared to 1 arm with many fingers
5. If your head can't see what your hands are doing, it limits your ability to use tools. So all aliens should have eyes (or comparable sensory organs) that can comfortably visualize whatever your alien is touching. A vision-like sense is also very helpful for developing reading and writing though not absolutely necessary. These organs should also be in a head containing the brain and all of your other major sensory organs since this improves processing and reaction time by putting them all closer to the brain. This is seen in nearly all complex life forms; so, assume aliens will be similar. Secondary neural ganglions may exist throughout the rest of the body to improve motor control like an octopus does, but the actually sensory processing and executive thought parts of the nervous system should be in a head.
6. If you can't locomote while carrying a heavy load, then this limits your ability to use large tools and to construct buildings, or even to gather wood for a fire. This is where the upright body plan of the humanoid really shines because humans can lift and move things very well. Centaur or Naga-like body plans may work well too. This will make body types without skeletons of any sort much more rare though because an upright body plan requires structure.
7. Avoid really good natural defenses. A tiger or a chameleon would have very little reason stop and make a spear, even if they could. So body designs that are just a little bit helpless without weapons and tools puts the evolutionary pressure on to develop weapon and tool use. Don't get me wrong: claws, fangs, venom, and active camouflage are are perfectly reasonable adaptations to have... just don't make them too perfect of versions of these adaptations.

1. Elder Races. While all of the above rules will apply to civilized races that have only been around for a little while like humans. Advanced civilizations that have existed for evolutionary timescales are more likely to break the rules. Once a civilization develops the ideas of separation of labor, welfare, and automation, genetic features that once would have been selected against may prove beneficial in unexpected ways. An alien adapted to sit in front of a computer all day may survive famines and plagues better if they can naturally walk. An alien that relies on cybernetic augmentation might be more likely to survive their surgical adaptation if they are born with diminutive or missing appendages. An alien that lives its life interfacing with neurojacking technologies might become more fit without the distractions of natural vision, hearing, etc. So, many things we typically see as disabilities could become a future specie's adaptations causing one or more of the above rules to get thrown out the window all together... though I would still expect some vestigial elements of their humanoid evolution: like eyes that can't see, ears that can't hear, etc.
2. Color and skin type. Fur, feather, scales, shells, exoskeletons, and others will all be evolved to deal with each alien's native environment and ancestral lineage. So, any choice is as believable as another. That said, remember that any alien that does not see in the visual light spectrum will likely be black, white, or clear skinned if it comes from a planet where being seen by human like eyes is a not issue. Or the inverse, they could be very ornately patterned (like parrots) if they live where only themselves and few other animals can see in the visible light spectrum.
3. Sensory Organs. Human eyes, ears, mouths, and noses don't even look that much like some other mammals, much less animals in general. Alien sensory organs may be shaped very differently than humans, and even work by other mechanisms all together, but still plan to slap most of them into a head, and have some analogue for sight and feeling because they need to be able to have a good sense of what they are working on when tooling.
4. Digestive organs. While it should be true that your aliens will typically have a way to consume food and expel waste, the organs for this can come in all shapes an sizes and these have no bearing on how smart or tool using your alien can be. Some aliens may throw up their waste instead of having a specialized anus. Some may have sideways mouths, mandibles, proboscis, fangs, tusks, beaks, etc. Some might even be primary producers and need to sit in a tanning bed or a nutrient bath to "eat"... though I expect this to be more rare due to the energy requirements of being a tool user.
5. Legs and Feet. While hands are a pretty specific requirement, there is a lot more room for variance with the feet. This part of the body could be pretty much any number of legs with any number of joints. It could even be serpentine or something completely alien. As long as your alien can move around while holding something kind of heavy, its bottom section should be fine.
6. Size. The human brain is far from the most size efficient an organic brain can be. Even using Earth base biology, a bird brain the size of an orange could out-perform the human brain; so, expect some aliens to be as small as a medium sized dog whereas others could be the size of an elephant.
7. Reproductive Methods. Most aliens should have some kind of sexual reproduction because this is necessary for animals with longer life cycles to evolve at any reasonable rate. That said, sex organs come in all shapes and sizes; so, even if two aliens look almost identical, from the waist up, their methods of insemination and gestation could be completely incompatible. Don't do more than 2 genders though. It is a bad trope because it automatically puts a species at a terrible competitive disadvantage. It should either be a form of hermaphrodite or bi-gendered.
8. Lifespan. While this may not change how an alien looks, I think it's worth bringing up. Most of your aliens should probably have a natural lifespan of at least 30 years to give them time to learn science and then apply it for long enough before dying to make the learning worth while. That said, there are exceptions that could make certain aliens live much shorter lives. You could have an alpha phenotype that lives a long time and does all the learning and science and stuff while most members of the species are just dumb worker/slave phenotypes that live much shorter lives. In this case, the alpha phenotype may not be humanoid at all. Or you could have an advanced system of genetic memory such that a member of a species might only live for a short while, but it has memories going back 100 generations. Or a third exception would be a hive mind where each member lives a short while, but the higher level thinking of the species is actually an emergent intelligence caused by the interactions of many smaller, weaker, minds.

While all these rules do not mean that the default should be exactly humanoid, it does mean that every advanced civilization should have a lot of common features with humanoids. Considering the specifications above, I think making ~25% of your aliens truly humanoid (2 arms, 2 legs, phalanges, etc.) is a good idea, but all of your advanced aliens should be "effectively" humanoid in terms of what their body plans can get accomplished, even if they get there by different means.

As for 25% of your races being not just humanoid, but mistakable for human... that is far less believable since coloration, skin type, size, etc. will likely vary too much for this. If this is a needed element in your story, then these races should all have a single progenerate race. So, if for example, Neanderthals developed space flight about 40,000 years ago, colonized 3 other worlds, and then their civilization collapsed, then you could have humans find other very human like races out there. But it would be obvious from the other 3 worlds' fossil records that they did not evolve on their own planets; so, making it a mysterious thing would be less believable.

1. Bilateral symmetry appears to be universally advantageous for complex organisms. There are very few examples of non-bilateral life on Earth that is more advanced than a starfish; so, assume this to be common elsewhere too. It also means that all of the below assertions should assume an even number of arms, legs, etc. Though throwing in 1 or 2 radially symmetrical races, or bilateral races with a central appendage creating an odd number could be believable too.
2. If you live in an aquatic environment, you can be smart, but never develop fire which means you will never develop chemistry, metallurgy, or ceramics or any of the other things that helped humans get out of the stone age. This means that nearly all of your aliens should be terrestrial or amphibious, and come from an oxygen rich planet.
3. If you don't have something like fingers, then you will be very dexterity limited in your tool use. Again, this caps you at a very primitive state. So, all of your aliens should have something like hands with multiple fingers. Something more tentacle like works too, but don't give them suckers because those require an aquatic environment to form a good seal.
4. If you have less than 2 arms, you will have a hard time manipulating objects against each-other. If you have more than 2 primary arms, then your arms will be strength limited compared to your size. Cleaving and hammering require a lot of force. Trying to strike with shoulders that are not perpendicular to your target means you rely on kenosis instead of momentum to drive the terminal impact. For this reason, most of your aliens should have 2 main, bilateral arms, plus maybe 2-4 smaller arms or arms that second as feet. More than 6 arms with no fingers might happen too, where the arms work together for grasping, but expect such an animal to require some kind of adaptation that allows it to perform very swift "snapping" actions with its hands to overcome the single shoulder limitation issue, or for all the arms to emerge from more or less the same part of the body.
5. If you can't see what your hands are doing, it limits your ability to use tools. So most aliens should have eyes (or comparable sensory organs) that can comfortably visualize whatever your alien is touching. A vision-like sense is also very helpful for developing reading and writing though not absolutely necessary. These organs should usually be in a head containing the brain and all of your other major sensory organs since this improves processing and reaction time by putting them all closer to the brain. This is seen in nearly all complex life forms; so, assume aliens will be similar. Secondary neural ganglions may exist throughout the rest of the body to improve motor control like an octopus does, but the actually sensory processing and executive thought parts of the nervous system should be in a head.
6. If you can't be motile while carrying a heavy load, then this limits your ability to use large tools and to construct buildings, or even to gather fuel for a fire. This is where the upright body plan of the humanoid really shines because humans can carry things very well. In fact humans can carry a load much farther than any of our Hominidae relatives despite being the proportionally weakest member of in the family. Centaur or Naga-like body plans may work well too. This will make body types without skeletons of any sort much more rare though because an upright body plan requires structure.
7. Avoid really good natural defenses. A tiger or a chameleon would have very little reason stop and make a spear, even if they could. So body designs that are just a little bit helpless without weapons and tools puts the evolutionary pressure on to develop weapon and tool use. Don't get me wrong: claws, fangs, venom, and active camouflage are are perfectly reasonable adaptations to have... just don't make them too perfect of versions of these adaptations.

1. Elder Races. While all of the above rules will apply to civilized races that have only been around for a little while like humans. Advanced civilizations that have existed for evolutionary timescales are more likely to break the rules. Once a civilization develops the ideas of separation of labor, welfare, automation, cybernetics, and gene-manipulation, genetic features that once would have been selected against may prove beneficial in unexpected ways. An alien adapted to sit in front of a computer all day may survive famines and plagues better than if they can naturally walk. An alien that relies on cybernetic augmentation might be more likely to survive their surgical adaptation if they are born with diminutive or missing appendages. An alien that lives its life interfacing with neurojacking technologies might become more fit without the distractions of natural vision, hearing, etc. Genetic augmentation might lead to a sort of polymorphic caste system where everyone's body is specialized to the task they are born for... So, many things we typically see as disabilities could become a future specie's adaptations causing one or more of the above rules to get thrown out the window all together... though I would still expect in most cases some vestigial elements of their humanoid evolution: like eyes that can't see, ears that can't hear, etc.
2. Color and skin type. Fur, feather, scales, shells, exoskeletons, and others will all be evolved to deal with each alien's native environment and ancestral lineage. So, any choice is as believable as another. That said, remember that any alien that does not see in the visual light spectrum will likely be black, white, or clear skinned if it comes from a planet where being seen by human like eyes is a not issue. Or the inverse, they could be very ornately patterned (like parrots) if they live where only themselves and few other animals can see in the visible light spectrum.
3. Sensory Organs. Human eyes, ears, mouths, and noses don't even look that much like some other mammals, much less animals in general. Alien sensory organs may be shaped very differently than humans, and even work by other mechanisms all together, but still plan to slap most of them into a head, and have some analogue for sight and feeling because they need to be able to have a good sense of what they are working on when tooling.
4. Digestive organs. While it should be true that your aliens will typically have a way to consume food and expel waste, the organs for this can come in all shapes an sizes and these have no bearing on how smart or tool using your alien can be. Some aliens may throw up their waste instead of having a specialized anus. Some may have sideways mouths, mandibles, proboscis, fangs, tusks, beaks, etc. Some might even be primary producers and need to sit in a tanning bed or a nutrient bath to "eat"... though I expect this to be more rare due to the energy requirements of being a tool user.
5. Legs and Feet. While hands are a pretty specific requirement, there is a lot more room for variance with the feet. This part of the body could be pretty much any number of legs with any number of joints. It could even be serpentine or something completely alien. As long as your alien can move around while holding something kind of heavy, its bottom section should be fine.
6. Size. The human brain is far from the most size efficient an organic brain can be. Even using Earth base biology, a bird brain the size of an orange could out-perform the human brain; so, expect some aliens to be as small as a medium sized dog whereas others could be the size of an elephant.
7. Reproductive Methods. Most aliens should have some kind of sexual reproduction because this is necessary for animals with longer life cycles to evolve at any reasonable rate. That said, sex organs come in all shapes and sizes; so, even if two aliens look almost identical, from the waist up, their methods of insemination and gestation could be completely incompatible. Don't do more than 2 genders though. It is a bad trope because it automatically puts a species at a terrible competitive disadvantage making it one of the least believable alien characteristics you typically see in sci-fi. Most aliens should be a form of hermaphrodite or bi-gendered with some being asexual.
8. Lifespan. While this may not change how an alien looks, I think it's worth bringing up. Most of your aliens should probably have a natural lifespan of at least 30 years to give them time to learn science and then apply it for long enough before dying to make the learning worth while. That said, there are exceptions that could make certain aliens live much shorter lives. You could have an alpha phenotype that lives a long time and does all the learning and science and stuff while most members of the species are just dumb worker/slave phenotypes that live much shorter lives. In this case, the alpha phenotype may not be humanoid at all. Or you could have an advanced system of genetic memory such that a member of a species might only live for a short while, but it has memories going back 100 generations. Or a third exception would be a hive mind where each member lives a short while, but the higher level thinking of the species is actually an emergent intelligence caused by the interactions of many smaller, weaker, minds.

While all these rules do not mean that the default should be exactly humanoid, it does mean that every advanced civilization should have a lot of common features with humanoids. Considering the specifications above, I think making ~25% of your aliens truly humanoid (2 arms, 2 legs, phalanges, etc.) is a good idea, but most of your advanced aliens should be "effectively" humanoid in terms of what their body plans can get accomplished, even if they get there by different means.

As for 25% of your races being not just humanoid, but mistakable for human... that is far less believable since coloration, skin type, size, etc. will likely vary too much for this. If this is a needed element in your story, then these races should all have a single progenerate race. So, if for example, Neanderthals developed space flight about 40,000 years ago, colonized 3 other worlds, and then their civilization collapsed, then you could have humans find other very human like races out there. But it would be obvious from the other 3 worlds' fossil records that they did not evolve on their own planets; so, making it a mysterious thing would be less believable. The other way to go would be to make them mistakable only to non-humanoid aliens. An average human might mistake a cuttlefish for an octopus despite thier glaring differences just because most of us lack a deep familiarity with cephalopods. Likewise a Gronkian might have a really hard time telling humanoids apart if humanoids are a thing he's only ever seen a few times in his high-school biology class 10 years ago.

A lifeform does not have to be humanoid to be intelligent, but being generally humanoid helps a LOT with tool use. On Earth, we have a few species of cephalopods, cetaceans, and avians that evolved advanced intelligence well before our human ancestors did, but they don't have the body plans to form an advanced civilization; so, thier intelligence seems to have capped at about where hominids were in the early stone age, while humanoids were able to keep going.

1. Elder Races. While all of the above rules will apply to civilized races that have only been around for a little while like humans. Advanced civilizations that have existed for evolutionary timescales are more likely to break the rules. Once a civilization develops the ideas of separation of labor, welfare, and automation, genetic features that once would have been selected against may prove beneficial in unexpected ways. An alien adapted to sit in front of a computer all day may survive famines and plagues better if they can naturally walk. An alien that relies on cybernetic augmentation might be more likely to survive thier surgical adaptation if they are born with diminutive or missing appendages. An alien that lives its life interfacing with neurojacking technologies might become more fit without the distractions of natural vision, hearing, etc. So, many things we typically see as disabilities could become a future specie's adaptations causing one or more of the above rules to get thrown out the window all together... though I would still expect some vestigial elements of their humanoid evolution: like eyes that can't see, ears that can't hear, etc.
2. Color and skin type. Fur, feather, scales, shells, exoskeletons, and others will all be evolved to deal with each alien's native environment and ancestral lineage. So, any choice is as believable as another. That said, remember that any alien that does not see in the visual light spectrum will likely be black, white, or clear skinned if it comes from a planet where being seen by human like eyes is a not issue. Or the inverse, they could be very ornately patterned (like parrots) if they live where only themselves and few other animals can see in the visible light spectrum.
3. Sensory Organs. Human eyes, ears, mouths, and noses don't even look that much like some other mammals, much less animals in general. Alien sensory organs may be shaped very differently than humans, and even work by other mechanisms all together, but still plan to slap most of them into a head, and have some analogue for sight and feeling because they need to be able to have a good sense of what they are working on when tooling.
4. Digestive organs. While it should be true that your aliens will typically have a way to consume food and expel waste, the organs for this can come in all shapes an sizes and these have no bearing on how smart or tool using your alien can be. Some aliens may throw up their waste instead of having a specialized anus. Some may have sideways mouths, mandibles, proboscis, fangs, tusks, beaks, etc. Some might even be primary producers and need to sit in a tanning bed or a nutrient bath to "eat"... though I expect this to be more rare due to the energy requirements of being a tool user.
5. Legs and Feet. While hands are a pretty specific requirement, there is a lot more room for variance with the feet. This part of the body could be pretty much any number of legs with any number of joints. It could even be serpentine or something completely alien. As long as your alien can move around while holding something kind of heavy, its bottom section should be fine.
6. Size. The human brain is far from the most size efficient an organic brain can be. Even using Earth base biology, a bird brain the size of an orange could out-perform the human brain; so, expect some aliens to be as small as a medium sized dog whereas others could be the size of an elephant.
7. Reproductive Methods. Most aliens should have some kind of sexual reproduction because this is necessary for animals with longer life cycles to evolve at any reasonable rate. That said, sex organs come in all shapes and sizes; so, even if two aliens look almost identical, from the waist up, their methods of insemination and gestation could be completely incompatible. Don't do more than 2 genders though. It is a bad trope because it automatically puts a species at a terrible competitive disadvantage. It should either be a form of hermaphrodite or bi-gendered.
8. Lifespan. While this may not change how an alien looks, I think it's worth bringing up. Most of your aliens should probably have a natural lifespan of at least 30 years to give them time to learn science and then apply it for long enough before dying to make the learning worth while. That said, there are exceptions that could make certain aliens live much shorter lives. You could have an alpha phenotype that lives a long time and does all the learning and science and stuff while most members of the species are just dumb worker/slave phenotypes that live much shorter lives. In this case, the alpha phenotype may not be humanoid at all. Or you could have an advanced system of genetic memory such that a member of a species might only live for a short while, but it has memories going back 100 generations. Or a third exception would be a hive mind where each member lives a short while, but the higher level thinking of the species is actually an emergent intelligence caused by the interactions of many smaller, weaker, minds.

As for 25% of your races being not just humanoid, but mistakable for human... that is far less believable since coloration, skin type, size, etc. will likely vary too much for this. If this is a needed element in your story, then these races should all have a single progenerate race. So, if for example, Neanderthals developed space flight about 40,000 years ago, colonized 3 other worlds, and then thier civilization collapsed, then you could have humans find other very human like races out there. But it would be obvious from the other 3 worlds' fossil records that they did not evolve on thier own planets; so, making it a mysterious thing would be less believable.

A lifeform does not have to be humanoid to be intelligent, but being generally humanoid helps a LOT with tool use. On Earth, we have a few species of cephalopods, cetaceans, and avians that evolved advanced intelligence well before our human ancestors did, but they don't have the body plans to form an advanced civilization; so, their intelligence seems to have capped at about where hominids were in the early stone age, while humanoids were able to keep going.

1. Elder Races. While all of the above rules will apply to civilized races that have only been around for a little while like humans. Advanced civilizations that have existed for evolutionary timescales are more likely to break the rules. Once a civilization develops the ideas of separation of labor, welfare, and automation, genetic features that once would have been selected against may prove beneficial in unexpected ways. An alien adapted to sit in front of a computer all day may survive famines and plagues better if they can naturally walk. An alien that relies on cybernetic augmentation might be more likely to survive their surgical adaptation if they are born with diminutive or missing appendages. An alien that lives its life interfacing with neurojacking technologies might become more fit without the distractions of natural vision, hearing, etc. So, many things we typically see as disabilities could become a future specie's adaptations causing one or more of the above rules to get thrown out the window all together... though I would still expect some vestigial elements of their humanoid evolution: like eyes that can't see, ears that can't hear, etc.
2. Color and skin type. Fur, feather, scales, shells, exoskeletons, and others will all be evolved to deal with each alien's native environment and ancestral lineage. So, any choice is as believable as another. That said, remember that any alien that does not see in the visual light spectrum will likely be black, white, or clear skinned if it comes from a planet where being seen by human like eyes is a not issue. Or the inverse, they could be very ornately patterned (like parrots) if they live where only themselves and few other animals can see in the visible light spectrum.
3. Sensory Organs. Human eyes, ears, mouths, and noses don't even look that much like some other mammals, much less animals in general. Alien sensory organs may be shaped very differently than humans, and even work by other mechanisms all together, but still plan to slap most of them into a head, and have some analogue for sight and feeling because they need to be able to have a good sense of what they are working on when tooling.
4. Digestive organs. While it should be true that your aliens will typically have a way to consume food and expel waste, the organs for this can come in all shapes an sizes and these have no bearing on how smart or tool using your alien can be. Some aliens may throw up their waste instead of having a specialized anus. Some may have sideways mouths, mandibles, proboscis, fangs, tusks, beaks, etc. Some might even be primary producers and need to sit in a tanning bed or a nutrient bath to "eat"... though I expect this to be more rare due to the energy requirements of being a tool user.
5. Legs and Feet. While hands are a pretty specific requirement, there is a lot more room for variance with the feet. This part of the body could be pretty much any number of legs with any number of joints. It could even be serpentine or something completely alien. As long as your alien can move around while holding something kind of heavy, its bottom section should be fine.
6. Size. The human brain is far from the most size efficient an organic brain can be. Even using Earth base biology, a bird brain the size of an orange could out-perform the human brain; so, expect some aliens to be as small as a medium sized dog whereas others could be the size of an elephant.
7. Reproductive Methods. Most aliens should have some kind of sexual reproduction because this is necessary for animals with longer life cycles to evolve at any reasonable rate. That said, sex organs come in all shapes and sizes; so, even if two aliens look almost identical, from the waist up, their methods of insemination and gestation could be completely incompatible. Don't do more than 2 genders though. It is a bad trope because it automatically puts a species at a terrible competitive disadvantage. It should either be a form of hermaphrodite or bi-gendered.
8. Lifespan. While this may not change how an alien looks, I think it's worth bringing up. Most of your aliens should probably have a natural lifespan of at least 30 years to give them time to learn science and then apply it for long enough before dying to make the learning worth while. That said, there are exceptions that could make certain aliens live much shorter lives. You could have an alpha phenotype that lives a long time and does all the learning and science and stuff while most members of the species are just dumb worker/slave phenotypes that live much shorter lives. In this case, the alpha phenotype may not be humanoid at all. Or you could have an advanced system of genetic memory such that a member of a species might only live for a short while, but it has memories going back 100 generations. Or a third exception would be a hive mind where each member lives a short while, but the higher level thinking of the species is actually an emergent intelligence caused by the interactions of many smaller, weaker, minds.

As for 25% of your races being not just humanoid, but mistakable for human... that is far less believable since coloration, skin type, size, etc. will likely vary too much for this. If this is a needed element in your story, then these races should all have a single progenerate race. So, if for example, Neanderthals developed space flight about 40,000 years ago, colonized 3 other worlds, and then their civilization collapsed, then you could have humans find other very human like races out there. But it would be obvious from the other 3 worlds' fossil records that they did not evolve on their own planets; so, making it a mysterious thing would be less believable.

1. Bilateral symmetry appears to be universally advantageous for complex organisms. There are very few examples of non-bilateral life on Earth that is more advanced than a starfish; so, assume this to be common elsewhere too. It also means that all of the below assertions should assume an even number of arms, legs, etc. Though throwing in 1 or 2 radially symmetrical races could be believable.
2. If you live in an aquatic environment, you can be smart, but never develop fire which means you will never develop chemistry, metallurgy, or ceramics or any of the other things that helped humans get out of the stone age. This means that nearly all of your aliens should be terrestrial or amphibious, and come from an oxygen rich planet.
3. If you don't have something like fingers, then you will be very dexterity limited in your tool use. Again, this caps you at a very primitive state. So, all of your aliens should have something like hands with multiple fingers. Something more tentacle like works too, but don't give them suckers because those require an aquatic environment to form a good seal.
4. If you have less than 2 arms, you will have a hard time manipulating objects against each-other and if you have more than 2 primary arms, then your arms will be strength limited compared to your size. So, most of your aliens should have 2 main arms, plus maybe 2-4 smaller arms or arms that second as feet. More than 6 arms with no fingers might happen too, where the arms work together for grasping, but expect that to be more rare since it wastes a lot more body mass on the extra appendages compared to 1 arm with many fingers
5. If your head can't see what your hands are doing, it limits your ability to use tools. So all aliens should have eyes (or comparable sensory organs) that can comfortably face whatever your alien is touching for hours on end. A vision-like sense is also very helpful for developing reading and writing though not absolutely necessary. These organs should also be in a head containing the brain and all of your other major sensory organs since this improves processing and reaction time by putting them all closer to the brain. This is seen in nearly all complex life forms; so, assume aliens will be similar. Secondary neural ganglions may exist throughout the rest of the body to improve motor control like an octopus does, but the actually sensory processing and executive thought parts of the nervous system should be in a head.
6. If you can't locomote while carrying a heavy load, then this limits your ability to use large tools and to construct buildings, or even to gather wood for a fire. This is where the upright body plan of the humanoid really shines because humans can lift and move things very well. Centaur or Naga-like body plans may work well too. This will make body types without skeletons of any sort much more rare though because an upright body plan requires structure.
7. Avoid really good natural defenses. A tiger or a chameleon would have very little reason stop and make a spear, even if they could, So body designs that are just a little bit helpless without weapons and tools puts the evolutionary pressure on to develop weapon and tool use. Don't get me wrong: claws, fangs, venom, and active camouflage are are perfectly reasonable adaptations to have... just don't make them too perfect of versions of these adaptations.

1. Elder Races. While all of the above rules will apply to civilized races that have only been around for a little while like humans. Advanced civilizations that have existed for evolutionary timescales are more likely to break the rules. Once a civilization develops the ideas of separation of labor and welfare, genetic features that once would have been selected against may prove beneficial in unexpected ways. An alien adapted to sit in front of a computer all day may survive famines and plagues better if they can't naturally walk. An alien that relies on cybernetic augmentation might be more likely to survive thier surgical adaptation if they are born with diminutive or missing appendages. An alien that lives its life interfacing with neurojacking technologies might become more fit without the distractions of vision, hearing, etc. So, many things we typically see as disabilities could become a future specie's adaptations causing one or more of the above rules to get thrown out the window all together... though I would still expect some vestigial elements of their humanoid evolution: like eyes that can't see, ears that can't hear, etc.
2. Color and skin type. Fur, feather, scales, shells, exoskeletons, and others will all be evolved to deal with each alien's native environment and ancestral lineage. So, any choice is as believable as another. That said, remember that any alien that does not see in the visual light spectrum will likely be black, white, or clear skinned if it comes from a planet where being seen by human like eyes is a not issue. Or the inverse, they could be very ornately patterned (like parrots) if they live where only themselves and few other animals can see in the visible light spectrum.
3. Sensory Organs. Human eyes, ears, mouths, and noses don't even look that much like some other mammals, much less animals in general. Alien sensory organs may be shaped very differently than humans, and even work by other mechanisms all together, but still plan to slap most of them into a head, and have some analogue for sight and feeling because they need to be able to have a good sense of what they are working on when tooling.
4. Digestive organs. While it should be true that your aliens will typically have a way to consume food and expel waste, the organs for this can come in all shapes an sizes and these have no bearing on how smart or tool using your alien can be. Some aliens may throw up their waste instead of having a specialized anus. Some may have sideways mouths, mandibles, proboscis, fangs, tusks, beaks, etc. Some might even be primary producers and need to sit in a tanning bed or a nutrient bath to "eat"... though I expect this to be more rare due to the energy requirements of being a tool user.
5. Legs and Feet. While hands are a pretty specific requirement, there is a lot more room for variance with the feet. This part of the body could be pretty much any number of legs with any number of joints. It could even be serpentine or something completely alien. As long as your alien can move around while holding something kind of heavy, its bottom section should be fine.
6. Size. The human brain is far from the most size efficient an organic brain can be. Even using Earth base biology, a bird brain the size of an orange could out-perform the human brain; so, expect some aliens to be as small as a medium sized dog whereas others could be the size of an elephant.
7. Reproductive Methods. Most aliens should have some kind of sexual reproduction because this is necessary for animals with longer life cycles to evolve at any reasonable rate. That said, sex organs come in all shapes and sizes; so, even if two aliens look almost identical, from the waist up, their methods of insemination and gestation could be completely incompatible. Don't do more than 2 genders though. It is a bad trope because it automatically puts a species at a terrible competitive disadvantage. It should either be a form of hermaphrodite or bi-gendered.
8. Lifespan. While this may not change how an alien looks, I think it's worth bringing up. Most of your aliens should probably have a natural lifespan of at least 30 years to give them time to learn science and then apply it for long enough before dying to make the learning worth while. That said, there are exceptions that could make certain aliens live much shorter lives. You could have an alpha phenotype that lives a long time and does all the learning and science and stuff while most members of the species are just dumb worker/slave phenotypes that live much shorter lives. In this case, the alpha phenotype may not be humanoid at all. Or you could have an advanced system of genetic memory such that a member of a species might only live for a short while, but it has memories going back 100 generations. Or a third exception would be a hive mind where each member lives a short while, but the higher level thinking of the species is actually an emergent intelligence caused by the interactions of many smaller, weaker, minds.

1. Bilateral symmetry appears to be universally advantageous for complex organisms. There are very few examples of non-bilateral life on Earth that is more advanced than a starfish; so, assume this to be common elsewhere too. It also means that all of the below assertions should assume an even number of arms, legs, etc. Though throwing in 1 or 2 radially symmetrical races, or bilateral races with a central appendage creating an odd number could be believable too.
2. If you live in an aquatic environment, you can be smart, but never develop fire which means you will never develop chemistry, metallurgy, or ceramics or any of the other things that helped humans get out of the stone age. This means that nearly all of your aliens should be terrestrial or amphibious, and come from an oxygen rich planet.
3. If you don't have something like fingers, then you will be very dexterity limited in your tool use. Again, this caps you at a very primitive state. So, all of your aliens should have something like hands with multiple fingers. Something more tentacle like works too, but don't give them suckers because those require an aquatic environment to form a good seal.
4. If you have less than 2 arms, you will have a hard time manipulating objects against each-other and if you have more than 2 primary arms, then your arms will be strength limited compared to your size. So, most of your aliens should have 2 main arms, plus maybe 2-4 smaller arms or arms that second as feet. More than 6 arms with no fingers might happen too, where the arms work together for grasping, but expect that to be more rare since it wastes a lot more body mass on the extra appendages compared to 1 arm with many fingers
5. If your head can't see what your hands are doing, it limits your ability to use tools. So all aliens should have eyes (or comparable sensory organs) that can comfortably visualize whatever your alien is touching. A vision-like sense is also very helpful for developing reading and writing though not absolutely necessary. These organs should also be in a head containing the brain and all of your other major sensory organs since this improves processing and reaction time by putting them all closer to the brain. This is seen in nearly all complex life forms; so, assume aliens will be similar. Secondary neural ganglions may exist throughout the rest of the body to improve motor control like an octopus does, but the actually sensory processing and executive thought parts of the nervous system should be in a head.
6. If you can't locomote while carrying a heavy load, then this limits your ability to use large tools and to construct buildings, or even to gather wood for a fire. This is where the upright body plan of the humanoid really shines because humans can lift and move things very well. Centaur or Naga-like body plans may work well too. This will make body types without skeletons of any sort much more rare though because an upright body plan requires structure.
7. Avoid really good natural defenses. A tiger or a chameleon would have very little reason stop and make a spear, even if they could. So body designs that are just a little bit helpless without weapons and tools puts the evolutionary pressure on to develop weapon and tool use. Don't get me wrong: claws, fangs, venom, and active camouflage are are perfectly reasonable adaptations to have... just don't make them too perfect of versions of these adaptations.

1. Elder Races. While all of the above rules will apply to civilized races that have only been around for a little while like humans. Advanced civilizations that have existed for evolutionary timescales are more likely to break the rules. Once a civilization develops the ideas of separation of labor, welfare, and automation, genetic features that once would have been selected against may prove beneficial in unexpected ways. An alien adapted to sit in front of a computer all day may survive famines and plagues better if they can naturally walk. An alien that relies on cybernetic augmentation might be more likely to survive thier surgical adaptation if they are born with diminutive or missing appendages. An alien that lives its life interfacing with neurojacking technologies might become more fit without the distractions of natural vision, hearing, etc. So, many things we typically see as disabilities could become a future specie's adaptations causing one or more of the above rules to get thrown out the window all together... though I would still expect some vestigial elements of their humanoid evolution: like eyes that can't see, ears that can't hear, etc.
2. Color and skin type. Fur, feather, scales, shells, exoskeletons, and others will all be evolved to deal with each alien's native environment and ancestral lineage. So, any choice is as believable as another. That said, remember that any alien that does not see in the visual light spectrum will likely be black, white, or clear skinned if it comes from a planet where being seen by human like eyes is a not issue. Or the inverse, they could be very ornately patterned (like parrots) if they live where only themselves and few other animals can see in the visible light spectrum.
3. Sensory Organs. Human eyes, ears, mouths, and noses don't even look that much like some other mammals, much less animals in general. Alien sensory organs may be shaped very differently than humans, and even work by other mechanisms all together, but still plan to slap most of them into a head, and have some analogue for sight and feeling because they need to be able to have a good sense of what they are working on when tooling.
4. Digestive organs. While it should be true that your aliens will typically have a way to consume food and expel waste, the organs for this can come in all shapes an sizes and these have no bearing on how smart or tool using your alien can be. Some aliens may throw up their waste instead of having a specialized anus. Some may have sideways mouths, mandibles, proboscis, fangs, tusks, beaks, etc. Some might even be primary producers and need to sit in a tanning bed or a nutrient bath to "eat"... though I expect this to be more rare due to the energy requirements of being a tool user.
5. Legs and Feet. While hands are a pretty specific requirement, there is a lot more room for variance with the feet. This part of the body could be pretty much any number of legs with any number of joints. It could even be serpentine or something completely alien. As long as your alien can move around while holding something kind of heavy, its bottom section should be fine.
6. Size. The human brain is far from the most size efficient an organic brain can be. Even using Earth base biology, a bird brain the size of an orange could out-perform the human brain; so, expect some aliens to be as small as a medium sized dog whereas others could be the size of an elephant.
7. Reproductive Methods. Most aliens should have some kind of sexual reproduction because this is necessary for animals with longer life cycles to evolve at any reasonable rate. That said, sex organs come in all shapes and sizes; so, even if two aliens look almost identical, from the waist up, their methods of insemination and gestation could be completely incompatible. Don't do more than 2 genders though. It is a bad trope because it automatically puts a species at a terrible competitive disadvantage. It should either be a form of hermaphrodite or bi-gendered.
8. Lifespan. While this may not change how an alien looks, I think it's worth bringing up. Most of your aliens should probably have a natural lifespan of at least 30 years to give them time to learn science and then apply it for long enough before dying to make the learning worth while. That said, there are exceptions that could make certain aliens live much shorter lives. You could have an alpha phenotype that lives a long time and does all the learning and science and stuff while most members of the species are just dumb worker/slave phenotypes that live much shorter lives. In this case, the alpha phenotype may not be humanoid at all. Or you could have an advanced system of genetic memory such that a member of a species might only live for a short while, but it has memories going back 100 generations. Or a third exception would be a hive mind where each member lives a short while, but the higher level thinking of the species is actually an emergent intelligence caused by the interactions of many smaller, weaker, minds.

As for 25% of your races being not just humanoid, but mistakable for human... that is far less believable since coloration, skin type, size, etc. will likely vary too much for this. If this is a needed element in your story, then these races should all have a single progenerate race. So, if for example, Neanderthals developed space flight about 40,000 years ago, colonized 3 other worlds, and then thier civilization collapsed, then you could have humans find other very human like races out there. But it would be obvious from the other 3 worlds' fossil records that they did not evolve on thier own planets; so, making it a mysterious thing would be less believable.