8 Possible Methods
An act of biological warfare planned extremely precisely may be able to wipe out the global population. It's not likely, but then again, nothing is likely to completely annihilate all of humanity; life finds a way.
If a virus, bacteria, or prion is designed to kill with the most efficient incubation period, methods of spread, etc. and planted in multiple countries (or even better spread by drones through the air near airports and in major cities across the world) it may be able to kill the population relatively quickly. As with all of these methods, people in isolated places like Antarctic research stations and the International Space Station will not die so quickly - it will have to be from a lack of resources.
Note that this pathogen must specifically be delivered to isolated places - remote islands, cruise ships, etc. to really kill everyone - but that those who survive may end their own lives.
It's also worth mentioning that an engineered pathogen need not worry about "natural immunity" - there are bound to be ways to bypass this if you can make the perfect biological weapon.
Similar to the above - however, this involves unintentional human actions creating a pathogen, which, by pure luck, conquers the planet. Very unlikely, but not impossible.
We're already creating "superbugs" every year by overusing antibiotics. In cramped, industrial sized farms, livestock in bacterial breeding grounds are pumped full of too-strong antibiotics. The bacteria that survive proliferate, and, when their ancestors are exposed to the new rounds of stronger antibiotics, the ones that survive reproduce, and so on - until we're left with multiple recorded cases of bacteria we don't know how to kill.
All it takes is a bacteria that can be transmitted to humans, with negative effects and high transmission - and the pure luck to kill us all.
A dispute between countries, or better yet countries with nuclear allies against countries with other nuclear allies, may cloak the planet in radiation. This would poison and kill much of the civilian population, and only a handful of people in bunkers would survive. Astronauts would starve before NASA could get them down, and Antarctic researchers would likely meet the same fate.
Those in bunkers likely wouldn't survive due to nuclear winter: clouds of soot would lower global temperatures, meaning people emerging from their bunkers (provided there was enough food) would not be able to farm efficiently. Additionally, it has been suggested that this type of event would destroy the ozone layer - showering the frozen Earth with deadly radiation, complicating or ending complex life for a very, very long time.
Overcrowding and Resource Mismanagement
Following some models of population growth, the Earth may run out of space and resources before we solve the problem of overpopulation itself. While this will cause mass deaths, the remaining population can still get by. Eventually, these cycles will deplete the Earth's natural resources. According to Stephen Hawking, we must leave Earth, or else this is what will end humanity.
The problem with leaving Earth after we consume it (think WALL-E) is that we do not have economically viable means to transport thousands, let alone millions or billions of people to another location - the majority of people will be left on Earth as the population starves.
Those not included in "the majority" may actually be doing fine, in a colony on Mars. In order for the colony to sustain itself without requiring materials from Earth, it must be able to mine for every possible mineral used in every computer or robot part, grow every type of food needed without new shipments, refine and process all materials, maintain electricity (nuclear batteries and solar panels only last so long), and find water (groundwater reserves are great but they may dry up), among other things. I wish these colonists luck, but it probably won't work out.
Grey Goo and Ecophagy
A slightly more "out there" approach. This suggests that we will develop the field of nanorobotics to the point that we create swarms of self-replicating machines. These swarms could, if not controlled, grow exponentially, devouring ecosystems in their quest to reproduce. Supposedly they may be able to sterilize the planet; whether this scenario is actually realistic is up to you.
A less depressing method, this suggests that humans will evolve over time until we become a new species - compare humans to our primate ancestors - which would technically mean humans "annihilated" themselves just by reproducing.
While this is a clever approach, it may be less likely than the above scenarios. Evolution favors isolated populations - see the biodiversity of the Galapagos Islands - because traits can be passed throughout the species relatively quickly. There are over seven billion of us, and we can travel anywhere, to reproduce with (evolutionwise) anyone. Any new changes made will be watered down, fast.
Additionally, humans don't need to change, so they may not. In a world where antibiotics and surgeries sustain those who can't cope with "survival of the fittest" we may not be pressured environmentally to adapt.
Another slightly out-there suggestion, although not impossible. This suggests that something like a nuclear weapon can trigger or speed up a supervolcanic eruption slated to occur soon. Such a release, multiplied by the number of supervolcanoes in the world, may be comparable to a nuclear winter, which, as described above, would be more than enough to wipe out humanity.
Pissing off the Neighbors
Very unlikely, but I'm including it for fun. If humans anger aliens with weapons of mass destruction - capable of sterilizing the Earth's surface - we will indirectly result in our own annihilation.