Disclaimer: This question uses some liberal wording to get key ideas across. It's not meant to be academically rigorous, so please try to focus on the ideas and not the exact definitions of the terms used. If you need clarification on something or have suggestions to make the wording clearer I'll be happy to add them.
Executive Summary: The goal of this question is to explore whether or not space-faring species would have many "humanoid" characteristics. Here are some key terms used in the question with explanations of what they mean and how they fit into the goal:
- Intelligent life - Life forms which have developed a higher degree of social complexity and demonstrated the potential to learn. For example, humans, dogs, birds and dolphins. Proposed species must meet this criteria, or you must provide a plausible explanation for why it is not required.
- Apex species - A species which has dominated its biosphere and kept competition to a minimum, or has a reasonable means of existing beside another dominant species (typically includes but is not limited to "apex predators"). For example, humans, tigers and orcas. Intelligence is a prerequisite unless you can plausibly explain why it is not required.
- Space-faring race - The ultimate goal of this question. A species which has the time and ability to construct methods for achieving space flight. Keep in mind a harsh environment would greatly impact their chances of surviving as a species long enough to do this. For clarity, things like insects are not a good candidate for this unless you can explain how they would achieve the intelligence prerequisite.
- Humanoid - Physically resembling a human pattern with two legs, two arms, a head containing sensory organs and possibly communication capability, etc.
There are plenty of theories on what intelligent life would look like on other worlds. Sci-fi creators go to great lengths to come up with aliens who are truly alien to us. But would an intelligent space-faring race really be anything other than generally "humanoid"? Would the universe actually have a reason to develop space-faring species other than rubber forehead aliens?
Consider the following (keeping in mind these are general descriptions and not strict definitions), and remember that evolution succeeds only when it is more efficient than the base:
Without fine manipulators we would not be able to use tools, and there's no sensible reason to develop tentacles on land so that only leaves hand-like clusters of extremities.
There's no conceivable need for more than two hands that wouldn't be outweighed by the inefficiency of having to supply them with energy.
Being bipedal gives us a combination of balance, fast/slow modes of travel, excellent ability to overcome obstacles and chase prey or escape predators.
Having more than two legs would imply a lack of hands due to efficiency constraints (how many intelligent creatures have you seen with 4 legs and 2 arms?)
A head containing the most critical sensory organs makes sense. Anything we've ever designed that's supposed to have good visibility is tall with all its sensor ability at the top (think air traffic control towers, lookout posts, etc).
Having the primary method of vocalization in the head also makes sense because the higher up it is, the better it will be at projecting sound (assuming sound is the main method of communication, thank for pointing that out @TimB).
Concentrating functions like eating/breathing/talking into one system is very efficient (again, virtually every organism we know of does this - certainly every dominant organism anyways)
Sure we can design all kinds of crazy adaptations to deal with environmental threats but do we have any reason at all to believe they would happen in reality (and evolve/survive to the point where they become space-faring species) beyond just "we want more flavor"?
The most variation I can conceive of would be skin composition, to allow for living in various elements. But I think ultimately the dominant species would evolve away from having seriously-protective skin features. After all, they would spend tens or hundreds of thousands of years using their intelligence to craft environmental stabilizers like clothing and shelter, so having fur or even just tough skin would have become unnecessary long ago.
We ultimately have had the chance to hone our intelligence to the point of making technological advances thanks to the fact that life on earth isn't that rough. If we were in a world full of constant threats or changing environments, chances are our evolutionary path would have taken us in the direction of physical survival instead of intelligent expansion (e.g., armor plating instead of a bigger brain).
TL;DR: Is there any truly convincing argument for an intelligent, space-faring species to not develop with very similar characteristics to humans? Or as put more appropriately by @Taemyr: "Do we have any reason to assume that any particular inteligent alien would have a markedly different body plan than homo sapiens?"
Edit: To be clear... I'm asking for fully-explained logic showing why a significantly different "style" of organism would end up not only being the dominant species on its planet, but be successful enough to develop space-faring technology. Please focus answers on plausible examples based as much in science as possible.