Well, it's hard to put a "villain" tag on the ones I do, even if they are... hm.
Okay, well, I'll just note that I LIKE Ravel from PS:T. Relate, no, but that game was hellishly good for twisting your emotions.
Relate... Ah, I have it. Griffin. The Invisible Man himself. He was no trouble at all until absolutely everyone picked and poked and pried at him and betrayed him. (The old friend near the end is a particularly assholish example of this. If he had just NOT betrayed him, kept calm, and tried to talk him down, this all could have been avoided!) He's not so much a villain as he is an unbalanced man who is driven insane by everyone around him. I totally get that.