Kefka, hands down. He actually succeeds at his goal of blighting the face of the planet and becoming a god. None of the other villains come even close. Plus, he doubles as comic relief. What's not to love?

That said, insert the obligatory disclaimer that I haven't played FFI-III, FFT, FFVIII, or FFXII.

I'd also consider the primary antagonists of FFVII to be Jenova and Hojo, not Sephiroth. Yes, I know what the Ultimania guide says, but honestly, smurf all this moneygrubbing sequel crap Square is releasing these days