Kuja is by far the most underrated villian. Everyone pretty much sees that he has a thong on and goes "ew! he sucks!" And they completely ignore pretty much all the chaos he cause in the game. I put him slightly behing Kefka, and I mean slight.
And then they think of stupid theories like ZOMG HE WUZ GIRL AND THEY TOOK OFF HIS BOOBS. I blame it on kids being raised on DBZ and Harry Potter so they don't know a good villain when they see one.
I think Sephiroth is way overrated. All he really did was destroy a town, stab a girl in the back, and send meteor towards the planet, which was destroyed and did not cause any real destruction. Compared to Kefka and Kuja, that almost seems minor. Rufus was a more effective villian than Sephiroth.
Rufus was a bastard, Sephi was a crybaby. Kefka ruined/conquered the world in VI, and in IX Kuja destroys (or at least blasts the shit out of) his home planet...WITHOUT the aid of a meteor or any fancy summons. And once Kuja found out his origin, he changed his plan to wiping out all of EXISTENCE. I mean that's pretty hardcore <.<