Rubicant is one of my favorites, too. I like how he heals you but at the same time he allows Edge's parents to be turned into zombies. That's a true villian.

List off the top of my head:

1. Kefka (VI)
2. Kuja (IX)
3. Rubicant (IV)
4. Rufus (VII)
5. Sephiroth (VII)
6. Ultros (VI)
7. Hojo (VII)
8. Seifer (VIII)
9. Golbez (though Kain was better as a heel too) (IV)
10. Dark Knight (II)