MJPollard said:

And what was in the room that contained the Doctor's greatest fear? (Room 11, of course.)

I think I know: Amy's grave, or her dead body.

That's what I thought too, and it would make sense considering the end. However, he really didn't look that afraid of what was inside; he just sort of smiled and said "Of course," like he knew that it was his fear but wasn't that afraid. The cloister bell probably wouldn't ring if just Amy died. If it was a dead Amy or Rory, then I would imagine it being silent and the Doctor looking serious.

My bets are on the universe being destroyed, the Daleks destroying all, time unraveling, him accidentally causing the destruction of all creation, or Omega returning... All of which would trigger the cloister bell.

In any case, what do you guys think, is Amy and Rory's departure permanent? There were rumors that this was Karen Gillian's last season.