Ugh, since I just joined this forum Im incredibly late to the party, but I agree with Sephiroth being up there... Kuja was pretty good too, and I loved the plot twist near the end of FF IX so that helps.. Kuja lacked the "big final boss monster" form though, which leads to that random Necron encounter, oh well

Ultimecia is up there too, although its the villain that gets the least air time in the whole series :P but still.. I love time related stuff and 1 - her castle kicks ass 2 - the final battle is awesome and the music rocks

FF IX garland was a very nice "villain", shame he wasnt the main one

Kefka was ridiculous, nuff said