I just checked it out too. I think we can write off the apple safely, since he uses it later in the episode to prove to Amy that he's real. "Everything's gonna be fine" is possible. As is the bit where he tells Amy that to close the crack he needs to open it all the way first.

I'm having some unformed ideas about this all, which are hard to put into words. Maybe it's not any specific thing he wants her to remember -- he tells her that's not the point, just that she has to remember. Something to do with memory and time being unwritten. Perhaps something will be unwritten that Amy needs to remember?

Skipped time. The clock in Amy's bedroom skips ahead a day for no apparent reason. The Doctor says he'll be back in five minutes, but it takes 12 years. An honest mistake in a new body with a new TARDIS? Or something else?

The duck pond. "What is THAT?" the Doctor cries. Amy tells him it's a duck pond. "Where are the ducks?" There are never any ducks. How do you know it's a duck pond? "I don't know, it just is. Is it important?" The Doctor doesn't know, then he has a regeneration episode and the show moves on. But then he mentions it again in the latest episode.

What's up with that duck pond? He obviously thought it was strange and important. It had no ducks, but everyone knew it was a duck pond. Thoughts, something to do with memory and time being unwritten. Something he missed, again. He keeps missing details that he thinks he should notice. A possibly future Doctor wants Amy to remember. Does remembering something make it so? She's getting married on the day the universe ends. Memory and time. Time can be unwritten. If you step in the crack, you never existed. You have to open it all the way to make it close. The Doctor in the TARDIS doesn't know. The Pandorica will open.

Yeah, I have no frigging idea.