Vaas from Far Cry 3. Always Vaas.
So much so that I wish he would've been the "final battle" in the game. Hoyt just didn't match up at all.
Definitely Logan from Fable III. He initially seems like a run-of-the-mill "evil tyrant" or whatever, but the things that are revealed about him near the end of the game make you reconsider your whole cause, whether you should actually have done the things you did.
They make you realize his interests are entirely noble, and that's what makes him unique and interesting as an antagonist.