I'm expecting this thread to be flooded with Sephiroth, but he's most certainly not MY favorite villain. Kuja from FF9 was the most vicious antagonist the Final Fantasy series ever had. The dude destroyed all four of the largest kingdoms on the planet, killed Queen Brahne after manipulating her for his evil plans, enslaved the entire Black mage race, and BLEW UP HIS HOME PLANET. No villain in Final Fantasy history can compare with that.