This poll is oddly lacking in options, I know for a fact my choice isn't on there.

Anyway, my favourite Final Fantasy villain is Kuja, without a doubt. I've never been a fan of Sephiroth, and there are too many people who seem to worship the ground he stepped on (just look at any FF forum), and especially when (SPOILER)he spends half the game asleep in the Northern Crater he isn't really a stunning villain. His appearance is hardly unique, either.

Kuja on the other hand worked as a successful villain. I've always liked magical villains as opposed to "look at me, I have a sword!" villains (probably why I liked Edea during FFVIII discs 1 and 2). Kuja's manipulation, his different attitude and attire (the latter of which some people just think he's a guy in drag. Yet if he was a female, I think we'd all know who they'd be looking for hentai of). The scenes at the end of Disc 3 of FFIX were just great, and Kuja caused a lot more death and destruction than numerous other FF villains.

Kefka is definitely an honourable mention (or should that be dishonourable?), as he worked well as a villain as well, and is deserving of second place. Twisted man who was just a bit off in the head was a great villain.

Edit: So of the three options, I guess I'll go with Kefka, despite preferring Kuja.