A big theme through "Series 5" was "Time can be re-written," and the finale wound up doing a big re-write of Series 5, so let's see if we can explain how it works:
- The Eleventh Hour Likely happens mainly as it was show, except Amy's family now lives with her. Presumably, when the Doctor meets Amelia, her family is asleep, and when he returns 12 years later, only Amy is home.
- The Beast Below Happens as shown, just now with no crack.
- Victory of the Daleks Happens as shown, just now with no crack. Amy might or might not remember the Dalek invasion of Earth.
- The Time of Angels/Flesh and Stone Without the crack present, it is hard to say what happened, unless they managed to trap the Angels again. Anyways, it's safe to say the Angels will be back.
- Vampires of Venice As the cracks didn't happen, either the Saturnians did not arrive in Venice, or they found another way. Difficult to say.
- Amy's Choice Happens as shown.
- The Hungry Earth/Cold Blood With no crack, Rory doesn't die, as the Doctor did not stop to investigate the crack, so they reached the TARDIS before Restac could shoot Rory.
- Vincent and the Doctor Happens as shown, Rory likely taking a minuscule role.
- The Lodger Happens as shown, Rory is on board the TARDIS to assist Amy now. (Drat. I'd love to see him and Amy shouting "KISS THE GIRL!")
- The Pandorica Opens/The Big Bang These now exist only in the memories of the Doctor, Amy, River, and possibly Rory. Because the TARDIS allows for paradoxical objects to exist inside, that is why the Doctor has River's vortex manipulator. The Doctor returns Amy and Rory to their homes in time for the wedding, but due to the side effects of the rewriting of Time, they forget the Doctor until River Song's gift reminds Amy, cuing the Doctor's entrance.
Okay. I'm done.