1. Kefka, from FFVI.
(He is, in fact, my favourite Final Fantasy character ever. "YOU SON OF A SUBMARINER!" I love his scenes and quotes oh so much, and the general insanity he has. Poisoning of Doma? Brilliant. Killing Leo? ;-;)
2.Gilgamesh, from FFV.
(Sure, he was a comic relief villain, but he's still great. "It's time to fight like men! And women! And women who dress like men!" <-- he has some great lines, lol, and is just generally awesome. I kinda felt sad when he died after turning good. Twas a shame. D=)
3. Sephiroth, from FFVII. (Yes, even with all the fanboys, I still like him. Hell, if I didn't like stuff just because of fanboys, I'd be insanely bored. Put simply, Seph's badass.)
4. Golbez, from FFIV.
(Sure, he wasn't the real villain, but I still love him, and the twist near the end when you find out his relation to Cecil. Probably also has something to do with the fact that FFIV is my second favourite in the series.)
5. Maquis, from FFTA2.
Right, so FFTA2's storyline failed... miserably, the gameplay was the highlight of the game. However, some of the side-stories aren't too bad. Sure they're not good enough to go into a main series game, but some were pretty good. Maquis was one of the Four Bosses of Duelhorn, a crime syndicate in FFTA2 that was trying to take over the country. Three of the four bosses were 'honourable villains', but villains nonetheless. Maquis was one of the good bosses, but his loyalty to Duelhorn was stronger. Eventually, when Duelhorn's pretty much lost, Maquis goes nuts and tries to finish the job on his own, that was a fun fight. Sure, he may not be particularly original, but I still like him enough for him to be in my top 5, even if he's not in the main story of TA2, let alone a main FF. >.>)