Top Three, Ranked from least favorite to most!
FF VI - Kefka, additedly, pulls most of the weight on this one for me. Utlros was good as well, though only for comic relief. And while the comedy is appriciated, doesn't really add much to the overall. The Empire, while being pretty Generic, were still done very well. Their reach and power were displayed quite well, and Ghestal had some great moments in terms of direct villlainy and being underhanded.
FF IV - As far as Story and motivation, I like Zemus. His turn to Zeroumus was... odd to say the least, but Zemus himself made a pretty efficient villain. Though Golbez and the Four Fiends are really the show stealers. A great variety of enemies, all of which come across as threatening for entirely different reasons. I think the threat of Baron may actually have been better presented the the threat of the FF VI empire on a whole. So while I think Kefka may be the single best villain among the two games, the overarching villany of FF IV gets wins this one.
FF IX - Kuja is already my favorite FF Villain. While he may be vain, narcasistic, and a terrible person all around, I kind of love his motivations. His entire motivation is to fight against a fate he has no control over, and what really makes him scary compared to other FF villains is not his wit, it's not his calm demenour or plans, it's the how insanely volatile his emotions can be.
Garland is absolutely wonderful as well, he fights to protect his people above all else. He's not evil, he simpley chose the lives of his people over the lives of Gaia.
And then you have Beatrix, who is a total bad ass. Like, oh dear god is she awesome.
I will give some credit to VII here though. While Sephiroth is the weak link of the games villains, Hojo is smurfing awesome up until that bit at the end where he's all 'Seph is my son and Imma help him!'. That was just... awkward. Had it not been for that moment, Hojo and SHinra may have put this game as a contender for my number 3 spot.