I actually pointed out on another thread like this several months ago that I too felt Hojo was a pretty evil, twisted person. He experimented on his wife (Which killed her), as well as his son, killed (we can assume) Vincent Valentine and preformed an operation on him that causes him to transform into a mindless beast when he is angry enough, killed Gast, tried to force-breed a human and a tigerlike creature, and tried to assist his son in destroying the world. Not to mention that he set into motion the events that nearly destroyed the world. (Experimenting on his son) Its kind of hard to say what caused him to do it. I mean, it obviously wasn't for fame, otherwise he would have let everyone know that he was Sephiroth's father. There doesn't appear to be a reason he would want to control the world. Of course, Hojo seemed to have been controlled partially by Jenova, at least during his experiment on his wife, but for that to have happened he would have to already have been at least slightly insane to begin with. I suppose he did it just for the advancement of science. Whatever his reasons are, he truely was very evil.

Dycedarg is also very underrated, and Kuja isn't necessarily the most evil, but I liked his style of manipulation the best.