I definetly agree about Kefka. He is without a doubt the most well written and colourful villins in videogame history. His insanity, while charming and funny at first, became scary and frightning. His plot twists, while almost obviouse that they would happen, left you with you're jaw on the floor. Even if you could see them comming a mile away it was the way he did these things that really shocked and apalled. Truely the greatest villin ever, not like that sissy Sephiroth.
I think another great villin was Lavos from Chrono Trigger. He was a very thought provoking character in a way. I suppose it being intellagent or not is up to debate but the impression that I got was that he was a parasite (not unlike a tick but on an enormus scale) and happend to land on our planet and simply acted out its nature.
The idea that a simple minded creature that runs purly on instinct and the drive to feed itself cuases a speed-up in human evolution just to nurture itself is very fasinating. And it also leads to great self doubt in characters wondering if they lived their lives for nothing if it was just to help feed a monster.
Fire Emblem: Path of Radiance also had some great villins, but if I tried to say why then it would only spoil the wonderful story.
