The fact that when Amy forgot Rory and looked at the Doctor, there would have been tears drying on her face and she would have no idea how they got there. This has been unsettling me since I saw the scene. In a good way--from a storytelling perspective, anyway--but still. I remain unsettled.
Though I do rather love that so much of the season has been about Amy's memory, about the inside of Amy's head. Prisoner Zero sets up that link with her, and it's her memory of what he/it looked like that helps to save the day. TBB is about her choosing to forget, but also choosing to remember--and choosing to remember the very thing, the Doctor, that she stubbornly remembered throughout her childhood. The Doctor tells her that she has to remember what he told her when she was seven, that it's important, but she has to remember it, not just be told. And now Rory (sob!), who has slipped out of her memories. And it's a bit peculiar, given how little we know about Amy in an overt sense. (What happened to her parents? Why did she decide to become a kissogram? etc.) Anyway, I am interested to see where this will all go.
In non-spoilery Doctor Who news, I'm amused that I'd totally forgotten that I used to keep trying to write stories about girls who had imaginary friends who weren't actually imaginary, until Amy Pond and her Raggedy Doctor.