The "Future Doctor" thing from 'Flesh and Stone' DOES happen, and has been confirmed by people who have seen the scripts.
The Pandorica has a rather useful feature, in that it keeps you alive... forever. (Which is good, considering what just happened to Amy.)
Amy has a very special brain because she grew up next to the crack for so long.
Auton-Rory is responsible for releasing the Doctor, and Amy gets locked inside the Pandorica while the Doctor goes off to find the right "fuel" to bring her back to life, leaving Rory to guard the box. Stuff happens and Rory is left waiting a LONG TIME, hence the "love that lasts a thousand years." He becomes "The Lone Centurion" and is spotted throughout time guarding the box. (and as some fans have pointed out, this actually makes him chronologically older than the Doctor now!)
Rory doesn't stay an Auton though, and he supposedly ends up human by the end.
The TARDIS does explode, but it's not how you think.
There is a wedding at the end, and one person who has seen the episode says that the ending is cheesily reminiscent of The Wizard of Oz.
Finally, there are some pretty strong indications that Omega shows up at the end. (possibly played by Jason Isaacs, aka Lucius Malfoy from the Harry Potter films) He may not be a traditional big bad though, and it's possible that his appearance is just a teaser for bigger events to occur in Series 6.
The main evidence in favor of the evil Time Lord's return come from two independent posters on Gallifrey Base; one who claims to have seen some concept art, and another who says that he was shown a suit of black "armor" with big gauntlets labled as "Omega." As for Jason Isaacs taking over the role, he was seen entering a closed door meeting with Steven Moffat, Mark Gatiss, and John Simm a few months back (after this episode was filmed, though). This led to much speculation that he could be taking over the role of the Master next year (or possibly just appearing in a future season of 'Sherlock', which Moffat and Gatiss also produce), but considering that another informant has teased that "a Harry Potter actor has a surprise role in the finale," some of that speculation has shifted towards him possibly being Omega instead.