Surprised that i'm the first to mention this, but this must be one of the only credit songs that have nearly made me cry. It just fits so well with the rest of the game, and sends your mind back over everything that's happened so far. And the teaser for another sequel at the end finishes it off nicely
http://www.youtube.com/watch?v=xAEjai3-T70
May not count, but You Have To Burn The Rope deserves a mention for surprising the hell out of me
http://www.youtube.com/watch?v=VmuiwOGi5gA
EDIT: Bear with me with non-embedded links, youtube trying to screw with me