Alright, I think I've waited long enough to discuss spoilers for this film.
;)
I rewatched it today, so here are some thoughts new and old:
I'm in the "everything was a dream" camp. The reason for this is because of the glaring plot hole regarding Limbo: There is no way to escape from it except to wait it out, yet Mal and Cobb seem to be able to wake up from it by simply killing themselves with a train. This is illogical, and throws everything else into question. For example, what kind of information regarding the rules of the dream should be trusted? I think that Cobb's account of how he and his wife got into Limbo is accurate to a point. They tried going deeper and deeper into the dream world, level by level until they reached bottom. But since a person cannot exit Limbo by dying, they simply must wait it out for however long they have been put under, which could expand into decades.
So it is clear that Mal and Cobb could not have actually woken up after the train incident. Everything after that is also a dream, but is Mal really present during the events of the movie? If they are both sharing a dream, why couldn't she attempt to contact him in the "real" world while he was trying to get back to his kids? The only way people sharing a dream can be entirely separated is if they are on different levels, and since a person can go no deeper than Limbo, the only explanation is that Mal was never in Limbo with Cobb, but instead is on a higher level of the original layered dream.
How were they separated? If they were to explore dreamspace together, and did so for a long time, there would be a real danger of one of them dying while under heavy sedation and dropping into Limbo without the other, leaving the other to return to wakefulness much quicker, at least from their point of view. This is how I interpret the events of the movie. Mal and Cobb were exploring dreamspace, Cobb was killed while they were sedated to go three levels down, and Mal was too afraid to go down after him, knowing that she may lose her mind down there. Cobb incorporated her into his Limbo however, and he built an entire world of (very similar) buildings. He lost his view of reality when he started building his memories (his memories, not hers) and the rest of the movie is him dealing with his emotional baggage of not spending time with his kids and trying to get back to some form of reality, as well as recognizing that the projection of his wife isn't real.
Incidentally, the totems are no use in determining whether you are or are not in a dream, for their behavior conforms to what you expect them to do. All they protect against is being fooled in another person's dream. Thus the movie is all Cobb's dream.
How's that for a necrobump?