Pain was a cool character but after I heard his goal it bumped him up pretty high on my villain scale. Strangely I can see the point of his philosophy.
Johan was one of the best manipulators I've ever read about. He could always make people do what he wanted and his goal seemed very evil. Plus, he could always pull a good plot twist when you least expected it.
I'd also like to recant Aizen. I only like him in the anime. When it's just text I roll my eyes at what he says but when it's voiced (and not the angry brooding homosexulal voice of the English dub) he becomes the character I like.