My list would almost exclusively contain various story elements in RPGs, probably topped by KotOR(yes, unbeveliable isn't it?):

SPOILER: If you don't want a major spoiling in KotOR, don't read.

The fact that the main character turned out to be the greatest Sith Lord in the galaxy made my jaw drop. I've seen such twists in books, but never implemented in a great way like this in a game.