[quote name='danny-o']The Great Mighty Poo[/quote]
Dude, Poo was on your side. Earthbound.
My favorite villain from an RPG was Ray from BoF2. This guy was a priest to Eva, who turned out to be a demon. Not that he was a really significant character, and he was surely not "evil", but his situation made me feel for him. I mean come on, to spend your whole life in servitude to a religion that turned out to be centered around an evil demon and refuse to give up your faith even when you knew about it, how sad is that.
Oh, also I was really impressed by the Transcendent One from Planescape: Torment. If your character was intelligent enough, you didn't have to fight him at all. Just convince him, through a rather long logical debate, that he is better off joining himself back to you.