A good question and I have several therories...
[LIST=1][*]River Song - remember that the Dr's and River's timelines are running in opposite directions.

In The Impossible Astronaut, River told Rory that she and the Doctor are meeting in reverse order and that every time she met him, he knew her less. She feared the day when she met a Doctor who did not know her. Which would be when she dies in Silence in the Library/Forest of the Dead.

When the 200 year older Dr confronts the spacesuit in 2011 he announces that he knows who is within.
[*]Amy Pond - after the crack in her wall, the crack following her across space and the duplicate bedroom in the orphanage it is a reasonable guess.[/LIST]
Next question is "Who is the Girl's Mother"[LIST=1][*]Amy Pond - the silence removed the chip so could remove the foestus presumably. Would also explain all the life support in the suit &c.
[*]River Song - It is obvious they are building the Romantic link between the Dr and River. Steven Moffat has dismissed the fan theory that River is a future version of Amy Pond, or that she is the Doctor's mother. Which can only make her the Dr's Lover, and does not rule her out for being Amy's Mum. River is also credited as being nearly human - i think Amy IS human.[/LIST]
Last thought.

The Dr is the father, Amy is the mother - no one recognises the girl, then she regenerates - does she regenerate into River Song.

No because then she would end up snogging her dad!

Has anyone else noticed in the end scene how the little girl seems unfazed by regeneration and how she looks at her hands as it starts (as did tennant/smith during their regeneration scenes).
Could she be a future doctor? Or the very first one (pre-hartnell)?

Or.. another time lord? Using the old fob-watch theory, an orpahan child finds the watch, keeps it safe, then BAM opens it and becomes a time lord..?
The Master? The bastard seems to always have a way out of everything, he's escaped the Time war once..

Then again.. the River theory is pretty awesome. She's been locked up for killing a great man.. maybe the doctor at the lake?

For me it's clearly Rory and Amy's child who as Amy and the Doctor discussed has become part timelord due to exposure to time travel, it explains why Amy is both pregnant and not pregnant at the same time. The only unexplained part is how the silence took Amy back in time to bring up the child to the age of what 5 or 6.