I'm not sure if anyone has braught it up, but Seiken Densetsu 3 is also Square Soft, I think O.o
Anyway, I think that the Dragon Lord / Prince of Darkness in Seiken Densetsu 3 were awesome villans. Basically, the Dragon Lord was this guy who died, but took this other guy with him, and gave him a bit of that power. Then all these other people were out to unleash the Mana spirits so that the Holy Land would open, the Dragon Lord or the Prince of Darkness would arrise and then destroy the Holy Land and claim the Sword of Mana, in turn killing the Mana Tree and the Goddess of Mana, who in the end actually did die.
Basically, either way, in the end, the Holy Land was destroyed. But at the end, in 1000 years time in which Mana would not exist till then, the Mana Tree will regrow and there will be a new goddess etc.
Anyway, besides that, I think Kefka and Sephiroth were the best SE villans.
Lavos didn't have enough personality, but he was great never the less.
Kefka, as said before, accomplished his goal, but was finished off. Sephiroth is hated and feared because he is so powerful, and because he killed Aeris and pretty much wanted the world destroyed.
And besides the main villans, I always loved FATE and the Dragon God. They just had such intricate plots. FATE was supposed to be the protector of humanity, yet attempted to reincarnate itself or make a new species of itself. And the Dragon God wanted the end of the humans, and the bastard took Harle :'(