Dunban from Xenoblade had a lot of badass moments.
The first time the third colossus raises its sword to strike you down in shadow of the colossus was totally badass. The moment is even better if Wander has been tossed to the side and struggling to get up as the sword falls, although it is more a moment of panic than badassery then.
I was not a big fan of the story mode in Soul Calibur 3, much preferring Chronicles of the Sword but a quote from one of the last bosses on an evil character's route was totally badass
Siegfried: If you have come for the sword don't expect to get out of here alive. Sorry to keep you, you're up next!
The line is totally cheesy to the extreme but works in that scene