This is not going to be exhaustive at all, but I keep noticing such moments as I am rewatching this series' episodes.
In "Flesh and Stone," the Doctor is fascinated by the crack in space/time, and spends a lot of time theorizing about it ("time can be rewritten," etc). But it seems to be linked, in his mind, with Amy and her wedding date (which is discovered to be the date of the event that caused the cracks in the first place). At the end of the episode, the Doctor pulls Amy into the TARDIS, chattering away about how "the most important thing in the universe is that I sort you out."
...which, judging by the next couple of episodes, seems to mean bringing Rory along and mending the Amy/Rory relationship. In "Vampires of Venice," nothing seems more important to the Doctor than making sure that Amy isn't spoiled for her upcoming marriage by allowing Rory to also experience the adventure of travels in time and space.
Then we have "Amy's Choice," which, again, is all about Amy. It's Amy who has to make the choice as to which reality they will die in, which reality isn't real (she chooses Rory; any world without Rory can't be real, she says). It's the Doctor who breaks them out of *both* dreams, but only after he's followed Amy's lead, and only because he knows who the Dream Lord is--a psychic manifestation of the Doctor's own dark side.
And it's the Dream Lord who placed the choice on Amy's shoulders, which means...what? That the Doctor's subconscious knows something very important about Amy (and her relationship with Rory?), something that his conscious self may not even know?
(Now I'm thinking of Lost. Rory is Amy's constant, y/n? *g*)
And that's not all!
I was startled by one line of dialogue at the end of "Cold Blood," as Amy is panicking over starting to forget Rory, and the Doctor is trying to help her hold onto those memories. Amy despairs, saying she can't do it. The Doctor responds, "You can, you can do it. I can't help you unless you do."
"I can't help you unless you do." What on earth does he mean by that? It could just be a way of saying, "I can't do it for you," but...why phrase it as the Doctor's aid being available but conditional on Amy's own ability to remember?
Does this go back to "Flesh and Stone"? Can the Doctor not sort Amy out unless she can remember Rory?
He does seem terribly insistent that she remember, during that scene, and the look on his face when he realizes she's completely forgotten is...dread? I don't know, I might be reading too much into that, but still.
And then, in "The Pandorica Opens," the Doctor actually asks Amy, "Haven't you ever wondered why your life doesn't make sense?" and it's a very specific question, a literal one, bearing on River's discoveries at Amy's Leadworth house.
Oh, I don't know. That's just what I've been pondering; what do you think about it?