Spoilers Behind The Cut! You were warned...
Right. All safe behind the zero-balance dwarf star alloy walls? Good.
So... here's the big questions we have so far.
Who Was Amy Really Thinking Of When She Was A Prisoner Of The Silence?
Any was taken prisoner but her nano-recorder was left behind, allowing Rory to hear her thoughts as she wishes for rescue. She later said that she was thinking of Rory when confronted about it but - as Rory pointed out - the person she was describing as wishing they would come to rescue her sounded like The Doctor, what with the "falling out of the sky and into her life" line.
Of course one could argue that Amy made her choice last season, making her feelings for Rory quite clear even before she finally married "stupid face". But is Amy being entirely honest with herself? She was certainly willing to run off with her childhood crush on her wedding day before AND tried to force The Doctor into some a most compromising position.
Rory seems to have taken her at her word. On the other hand...
What's Up With Rory And Amy's Memories?
Rory and The Doctor briefly discussed the burning of Rome - an incident they were both present for. The Doctor was there in his first incarnation and was indirectly responsible for starting the Great Roman Fire whereas Rory, as an Auton, was guarding The Pandorica. It is then that Rory reveals that while he has knowledge of what he did during the 2000 years he was guarding the Pandorica, the memories feel incomplete... like something he was told about rather than something he actually lived through.
Amy has a different problem, having lost several days of memory while being held by The Silence. Actually, given that her memory would have blanked every time she saw one and looked away, she could have been there much longer. Which raises the question of...
What's Up With Amy's Pregnancy?
At the end of The Impossible Astronaut, Amy told The Doctor that she was pregnant. Later, when he confronts her on the statement, she backtracks, saying that she was just worried about whether or not traveling in the TARDIS while pregnant might have negative side-effects. The Doctor then runs the TARDIS scanner... which keeps jumping between YES and NO on the pregnancy issue.
It's worth noting that, when Amy was investigating the orphanage earlier in the episode, she found a room with several pictures of a girl - the same girl that was in the space suit earlier. One of the pictures depicts Amy holding a baby and the picture makes Amy truly afraid and nervous even before The Silence show up and take her.
This brings us, naturally to...
Who Is The Impossible Astronaut/Little Girl?
With all the invoking of the standard tropes regarding American urban legends of Men In Black and Alien Abductions - particularly the legends regarding women being impregnated to create alien hybrid babies, it's no small wonder that the most popular theory thus far is that The Silence took Amy's baby and experimented on her for their own nefarious reasons. And yet... that's just one idea. So in no particular order, here's every idea I've had and heard.
1. The Little Girl is Amy and Rory's daughter, augmented by the technology of The Silence.
2. The Little Girl is Amy and The Doctor's daughter, who has inherited her fathers superhuman strength and regenerative powers.
3. The Little Girl is a young River Song.
4. The Little Girl is the daughter of River Song and The Doctor from THE FUTURE!
5. The Little Girl is a clone created by The Silence in an attempt to create their own Time Lords.
6. The Little Girl is just some random orphan who was kidnapped and experimented on by The Silence.
7. The Little Girl is a Time Lord child kidnapped by The Silence before the Time War, kept hidden from The Doctor all this time.
8. The Little Girl is The Lindbergh Baby.
Any questions? Any answers? Post them below.