Before I offer up what actually happened in the film, I'm going to summarize a couple of the more prominent theories floating around (skip past the blue if you don't want to read them):
The first theory is really an either or statement and is quite simplistic. Either Cobb made it back or he got lost in limbo. This all depends on whether the top simply wobbled and restored itself or if it wobbled and fell over. Thanks to Nolan's early cut, no one will ever know. This theory is fine for any normal movie-goer, and it is enough to satisfy the mental hunger of most people who realize that this film is a work of fiction. The important thing to understand was that Cobb walked away from the top without waiting to see what happened. He was happy and that's all that mattered.
For those of us who have significantly more free time, (putting aside Cobb's nonchalant attitude at the end) deeper and more complicated theories arise. The two most intriguing ones I have heard concern Saito. According to the first theory, Cobb is stuck in a prison of his own mind, and Saito was the real Inception artist. Saito's goal was to plant the idea in Cobb's mind that would allow him to get over Mal's death. At the end, Saito succeeds and Cobb is reunited with his father (Saito's employer). All the other passengers on the plane were either working with Saito or were just projections of Cobb's memory after seeing them on the plane. While this theory is definitely intriguing, I find it hard to believe for a number of reasons including the fact that no one is hooked up to any machine when Cobb wakes up in the plane.
In the second Saito theory, Cobb is the subject again. However, instead of helping him overcome something in the real world, the point of the job was to make Cobb realize he was dreaming. Saito tried his best, but Cobb's defenses were too much for him, and only the final moments in limbo with him as an old man indicate that Cobb is a lost cause. Saito makes it out, but Cobb is lost forever in a limbo that is finally a happy one for him. This theory also has a host of its issues (like if it's Saito's limbo, why does it look like Cobb's world?), but I find it to be more solid than the previous one.
I could recount all the theories I have heard, but that would take ages. As it is, I hardly did a good job on the previous two as I left out much of the detail concerned with each. In any case, they are not my theories, so feel free to blast them however you wish.
And while we are on the subject, some notably disastrous theories include Cobb's father performing the Inception, Cobb performing the Inception on himself, the kids performing the Inception, and limbo actually being the real world.
Now that we have those out of the way, here are my thoughts on the matter:
As the film states, Mal and Cobb went deeper and deeper until they got stuck in limbo. There, they had to figure out a way to escape and came up with the solution of the train running over their heads. The plan apparently succeeded, and they woke up, but Mal was never the same again. She committed suicide, convinced that she was still in a dream, and Cobb was overcome by guilt that he had planted the idea into her mind. This guilt manifests itself in the frequent sightings of his Mal projection and threatens to take over his mind. This is the biggest problem with Cobb on a surface level.
However, I say that this surface-level truth is actually all a lie. Have you ever wondered why Cobb and Mal were shown as old people in limbo before they escaped but not when they actually escaped? Yes, that's right, the scene where the train helps them escape limbo shows both Cobb and Mal in their real life ages, not their accelerated limbo ages. The reason behind this is that there is no limbo.
WHAT??? Are you saying Nolan blatantly lied to us just to make his film more confusing??? No, he did not. Cobb was the first person to introduce the concept of limbo. (You'll see why this is significant when I tell you later.) It was only after that initial statement that some of the others picked up on the idea.
So, if they weren't in limbo they were in the real world like that "disastrous theory" right? No. They weren't in the real world either. You can't create buildings out of thin air in real life, can you? Both Mal and Cobb were still in a dream, just a deeper state. They couldn't fathom the idea of ever going deeper than that, so they never tried. That assumption lead to the belief that limbo existed and no deeper progress was possible.
Why the absence of limbo is important is really just one thing: Without limbo, there is no "shared space." If it's not limbo, it obviously has to be the inner workings of ONE person's mind, and that person is Cobb. The imagined limbo is really the deepest level explored in Cobb's mind/dreams.
That is why Cobb and Mal appear to be young before the train hits. Cobb either gets his kick or naturally wakes up from that dream level back into a shallower state of sleep. This shallower state is what I like to call coma level, otherwise called reality by others. Mal is just as duped by the shift in dream levels as Cobb is, but she eventually realizes that she is still stuck in a dream. She tries to convince Cobb of this, but he is convinced he is in reality. Mal, no longer able to live in a world she knows as fake, jumps off the ledge and kicks herself back into reality, leaving Cobb behind.
While in this state of coma, Cobb has impenetrable defenses of his own mind, so no one can alter the reality he has set up. It is also the reason why he cannot be the architect in a deeper level - he is already the fully invested architect of this level. However, deeper states of dreaming, which he apparently has the ability to shift in and out of, leave him more vulnerable to outside penetration. Mal attempts to bring him back on multiple occasions, but she cannot succeed because Cobb believes her to be dead. That is why she turns to the help of others.
Cobb is, indeed, the subject of the Inception. The first step of the job begins when he receives the plane ticket and leaves his children (who are actually just projections of his mind standing in for his real children). It is obvious that this cannot be reality. Cobb is being chased by powerful unnamed corporations because he is accused of killing his wife. To any sane man, this makes no sense whatsoever. However, I digress.
Once the job has begun, all the members of Cobb's team (including Saito) are actually working for Mal. They progress through the stages of Cobb's mind to get to the root of the problem: the dream state referred to as limbo. If they can gain access to the deepest parts of his mind, they may be able to save him yet.
Wait, I thought the different levels were different team members dreaming? No. Nolan never acknowledges this in the film, so there is really no basis for that kind of thinking. The reason that one person stays behind each time is to ensure that Cobb's mental defenses do not overcome them while they are in a deeper state. This one person basically takes the responsibility of defending against Cobb as well as synchronizing the escape through that level.
As the team delves deeper, Mal is able to penetrate more easily until they reach the dream state referred to as limbo. Here, Mal has only one chance to get things done. If she cannot convince Cobb, it is highly unlikely that she will ever get a chance to come this deep again. In a last ditch effort, Mal attempts to convince Cobb again even stating that they remain in "limbo" together in the hopes that she will eventually free Cobb from there. However, Cobb is too far gone at that point, and his mind takes full defensive action kicking everyone out. What results is a sheltered world within Cobb's mind, in which he has finally overcome Mal's "death." He is finally able to see his children's faces, and he is happy. Still comatose, but happy...
So he didn't make it back to reality in the end? No, sadly, he did not. A dead giveaway is the surreal feeling of the film culminating in his children crouching in the exact same positions as his memories from before. The fact that they are slightly older and dressed slightly differently is only a result of of this new sheltered world distinguishing itself from the other penetrable world Cobb had been so accustomed to. I'm sure the children crouching is a memory from his real life, but I doubt it has anything to do with the actual chronology of the film.
With that said, the film is really a story about growth. It chronicles the growth of one man from doubt to certainty. When the film begins, Cobb denies the death of Mal, but by the end of the film, he accepts her death as a certainty. While this may not be reality, Cobb's decision to choose this belief causes it to become his reality. Nolan makes a brilliant statement with the film: perception is reality, and truth is relevant.
Congrats, Mr. Nolan, on making our minds question and our impulses excite. You get an A for this film - near perfection in my book...