I may be right out on a limb here but I've just put some things together that have been nagging at me about this season so far and come up with a theory.
It started with that scene where the Doctor escapes the Angels by slipping out of his jacket. Knowing Moffat never writes a scene without a purpose I wondered why the Doctor needed to lose his jacket at this point in the plot.
Next scene he leaves Amy with the soldier/clerics and then comes back briefly to tell her to remember what he said to her when she was seven? Why was he wearing his jacket? He'd lost it to the Angels and at no stage throughout the rest of the episode was he wearing it. Except there.
Continuity error? from this production team? I think not.
There's some wibbly wobbly timey wimey shennanigans going on here. Look at that scene. The Doctor's hair is untousled, he's wearing the jacket and the unexpectedness of it all is jarring. There's also suddenly more echo on his voice, and a forehead kiss that means those two or three lines suddenly mean a lot more to him.
With me so far? Now, think back to episode one.
After defeating the Atraxi the Doctor gets in the Tardis and leaves nineteen year-old Amy in the garden. Then we cut to her sitting on her suitcase in the same spot when she's seven, but not in the nighttime, in daylight. The Tardis engines sound and she looks up with a smile on her face. Then we get another jump cut edit to adult Amy in bed, waking when she hears the Tardis engines.
So, did the Doc return to Amy when she was seven and she just forgot all about it? Or is she having a dream about waiting for him as a child, and that dream is inspired by the reality of the Tardis making its (brakes on) noise as it appears outside her bedroom.
On first viewing that seems to be the case but...taken with that anomalous continuity jump in this weeks episode I think this is what's going on -
In the season finale the Doctor will end up jumping back into Amy's timeline and planting the seeds of something in her head, to help deal with whatever's coming. And the crack is either the consequence of that meddling, or the problem that he needs to solve by doing so.
And this ties into the 'fairy tale' alternate reality that Amy's over-active imagination has created. 'The Raggedy Doctor Universe' if you like.
And the clue is -
How do you know it's a duck pond if there aren't any ducks in it?
Episode one -
Doctor: And WHAT is that?"
Amy : It's a duck pond"
Doctor: Then why aren't there any ducks in it?
Amy: There's never been any ducks
Doctor: Then how do you know it's a duck pond?
Amy: Is it important?"
Doctor: I don't know. Why would I know?
Is it that there's never been any ducks? Like there's never been any Daleks? Like there's never been any clerics watching Amy in the woods?
When Amy finally gets back into The Tardis, she asks The Doctor why he picked her out of everyone. He tells her there's no reason and that it's just that he's lonely and needs a bit of fun. She asks if that's all and he says yes it is. Right in front of a graphic depiction of the crack in her wall on the Tardis display monitor.
He knows something here that he's not letting on, and it's very possible his time away has not just been spent on a quick trip around the moon.
So when they're in the forest and things are about to start getting erased from history there's this little exchange...
Episode Five
Doctor: Remember what I told you when I was seven.
Amy: What did you tell me?
Doctor: That's not the point
So what is the point?
Is it that the fact she doesn't remember and nor do we. We haven't heard him give her any advice when she was seven. He's yet to go back and give it.
Wibbly wobbly timey wimey. I'm loving this season!