To me, it's between Kefka, Sephiroth, and Kuja.
If I wanted to take the easy way out, I could just pick Sephy. He was definitely very bad ass, and I remember seeing that timeless image of him walking through the flames of Nibelheim for the very first time. I could swear he was the devil!!! But if you really stop and think about it, what exactly was Sephiroth's motivation for the things he did??? His goals were always crystal clear (summoning "meteor"), but the things that drove him to wanting the goal in the first place were never clear. Sure, you can argue that "HE'S CRAZY, THAT'S WHY!!!", but still...
Then there's Kekfa, IMO the most evil man in video game history. These are just one of those villains that are so easy to hate. He was like a little spirte-based Hitler in his ways, and that laugh... But then that's also a downfall. Kekfa is SO evil, it can actually be perceived as a bit ridiculous, even humorous at times. That's takes away some of his thunder.
And finally, Kuja. Definitely the most underrated villain if anything, I think square managed to combine Seph's "bad assness" and Kekfa's pure, unadulterated "evilness", and capture it in the form of this character. And plus, he's got that personal dragon with him! How could you compete with that? VERY cool baddy indeed, but then comes his downfall... his looks... I know the Japanese might be keen on the whole "super effeminate, gender confsuion" bit, but I am not. Kuja lost some points there. So, who do I choose???... Anyway, have fun voting!!!
P.S. If it seems like some of the "villains" listed for the older generation ff's are just the names of the last things you fight, it is because they are!!! I haven't played the ff's before FF5, so correct me if I named the wrong villain for a certain game...