After the events of episode 'The Big Bang', the Doctor has 'rebooted' the universe and is only brought back by Amy remembering him. It seems that those that were with him during those events retained their memories of the previous incarnation of the universe, but technically none of it ever happened.
As the Doctor himself says in 'A Good Man Goes to War', Amy and Rory's first time in the TARDIS in this universe was on their wedding night. So everything that happened previously is just a memory, just a story.
This question is kind of hinted at in other questions/answers, but I thought I'd ask it directly.
I can't remember exactly how he stated it, but before the new universe, when he is traveling back through his own time he says he has to step out of time, or remove himself from the universe, something like that.
How does that work? I guess you could call timey-wimey on him not being born in the universe, but then what happens to all of his past exploits? And what about his part in the time-war? Does all of that come back in some capacity when Amy pulls him back into the universe? How that would exclude events with Amy and Rory... well I have a headache now.