There are different theories out on the web why River Song is in prison.
I think the one which most of the people believe in is, that she was the one who killed the Doctor. But was it really her in this spacesuit in the episode "The Impossible Astronaut"? I really don't know. It could have been her because they are always meeting in the wrong order and she must have been a child when they've met for the first time.
River seems to have Timelord DNA but is she also able to regenerate or maybe regenerate just once? That's also something that puzzles me and I have heard different theories about it. Is River the girl we have seen in "Day of the Moon"?
I have read a comment lately that it's possible that we haven't seen the real Doctor die but a Ganger of him. That makes some sense but the technology must be more advanced then because normally the Gangers just disintegrate when they die.
Well, there are still a lot of questions we need and want an answer to concerning River and the Doctor. Please, vote in my new poll which is also about this theme.
One thing that also won't go out of my mind is how sad it must be for the Doctor to know how River dies all the time. That must be quite a burden for him.