Ultimecia was one (a pretty "glitchy" one -_-), St Ajora was one, Dark Cloud was one...

Kuja is a man, damn it! He hits o Dagger! He is just too androgine! o_o He is much prettier than Ultimecia though *shot*

And Adel is sort of a villain. But Adel doesn't count. If Kuja is a girl, Adel is a boy. Period.