I'm going to have to vote for Kefka, considering he was the only villain who had no means of ruling the world but to simply poison it and kill it, everyone on the planet including himself (as per his original plan). All other villains wanted pure power to rule over the planet/cosmos etc etc etc.
I think that anyone who isn't afraid to die to completely wipe out the planet and leave it at that, is quite a bit more dangerous than anything else lol.