Honestly, nothing scared me.
But if I had to choose one part of the game that shocked me a bit was first encountering the regenerators.
Oh, and another one would be down at the commando area where your in a kitchen, and then out of nowhere a ganado bursts out of the oven :S
I just witnessed the dred of oven man.
[Edited by shiguretheperv, 9/3/2009 7:12:29 PM]