The one that really jumps out at me is Kefka, probably because I really hated him in the game. Although I guess I hated Sephiroth for killing Aeris too (who was my favorite character in the game to that point, and really the back-bone of my party).
I am suprised that I am picking FF characters though, since I am not that big of a fan of them. I guess they just did a better job at making the main villians truly memorable than other games. (Although the villain for FF1 was one of the least memorable villains of the RPGs I have played.)
I just started playing BG1 for the first time the other day, I bought it with BG2 and am starting to make my way through the game. Maybe I will have a new favorite villain by the time I am done.