Kefka wins this easily.
Pure evil.
Nihilistic.
He's a character that actually has....character.
Came with a truly unique fashion sense.
Has a laugh that still sends a chill down my spine.
Set out and actually accomplished what he wanted to do.
He's just an extremely well thought-out character.
Truly the greatest villain of all time in my opinion, although I started playing the Final Fantasies from the start.
Now, let's take a look at Seph-
Emo.
Mama's boy.
Keeps a school girl's outfit in his closet.
..That's really about all he has going for him.
Don't get me wrong, FF7 was a good game too, but in comparing villains Seph doesn't stand a chance.
Here's proof.
http://www.youtube.com/watch?v=CMZBCQzmHa8
Yes, most people who think Seph is the best villain only think that because 7 is the first one they played, it's just their loss that they weren't old enough to enjoy the earlier games during their reign.
http://www.youtube.com/watch?v=CUiPJTB4P8s&NR=1 Another vid of Kefka owning Seph,

that cheap look, voices can be kind of annoying but it's pretty funny still.