I interrupt my recent "spate" of DC Comics-related posts to deal with Doctor Who, which is almost up to its last episode of the season (or series, as they call it in England). So, before the big finale answers any of my nagging suspicions, here are my own theories as to what might be going on. Bear in mind that only some of these can even be true, as they are not all compatible theories.
1. River Song could become the new Doctor. River Song is, apparently, a popular companion as well as beloved creation of the executive producer from back when he was only writing scripts in the Tennant years. The big reveal at mid-season was that River Song is a Time Lord. We've also had repeated reminders this season that River is a doctor in archaeology. So could she become The Doctor? We've been thinking ever since episode 1 this season that there has to be some way around the Doctor's demise, but if there isn't, than this is the way the series would continue. The hang-up here is that Matt Smith is also very popular, if not the most popular Doctor yet, so it would seem foolish to replace him...
2. The Silence (Silents?) are actually on the Doctor's side. Yes, we've been told these were the new villains, they look like villains, but what have they really done to menace our heroes other than a lot of posturing? They even tipped off the Doctor to their plans by alerting Amy. What did that accomplish, but to allow the Doctor to free baby Melody from them? And can it be only coincidence that Melody goes on to become River and almost kill the Doctor in 1943 only after escaping from the Silents? It seems they weren't incubating her in that spacesuit so much as holding her prisoner so she couldn't carry out her destiny.
I particularly like this theory because, not only is it such a big twist, but it kind of explains how the Doctor has always been able to use coincidence and luck to defeat his enemies over the years -- he's had a secret society of the Silents aiding him all this time that he can't remember having encountered after they help him. The downside of this theory, of course, is that it robs the Doctor of some of his glory by suggesting he's always had more companions than we knew.
3. The Doctor has been behind this all along. Remember River warning the Doctor that, if he didn't change his ways, that the universe would fear him as its greatest warrior? Well, what if the Doctor agrees and has been secretly arranging events so that he can fake his own death? With everyone thinking he's irrevocably dead, he can go back to helping people anonymously through time and space. Of course, the hang-up of this theory is that it still doesn't explain how he possibly faked being shot and then incinerated. And yet...
4. River was lying at the scene of the Doctor's death. River told Amy and Rory that the Doctor died because he was shot while regenerating. But "later", in 1943, River is shot multiple times after a mortal wound and still regenerates. So, is it the nature of the weapon, rather than the timing of the shots, that matters, or was she just lying about how you can kill a Time Lord...?