Viper, pardon the nitpicking, but you might want to look up what "penultimate" actually means before using it. It means "second-to-last" (ie: Eve is the penultimate boss of Parasite Eve; her son, "The Ultimate Being", is the final boss). Also, there's no hyphen in the word.
As for my not-by-any-means-comprehensive contributions:
Count Vlad Tepes Dracula (nearly every Castlevania title)
- The Prince of Darkness who makes his opponents question if they're really doing the work of God as they claim with an unshakable air of dignity and class surrounding him. Ironically, his awakened human form is far more dangerous than his many, many demonic incarnations.
Ganondorf / Ganon (every odd-numbered The Legend of Zelda title)
- Needs no introduction. The Ocarina of Time version is one of the few final battles for which the word "epic" can be used without hyperbole.
Kefka Pallazzo (Final Fantasy VI)
- Face it: when was the last time you saw a villain try to destroy the world, and SUCCEED!? Every single one of your party members must recover their nearly-non-existent will to live and tattered resolve to fight before even thinking of taking this "clown" down. A batshit insane sociopath, and he's loving every minute of it. Basically, Square's answer to The Joker.
Galbalan / Galvaran (Ys ~The Oath in Felghana~)
- Synthetic lifeform loses his sanity and swears vengeance against his creators, turning himself into a God in the process. Easily has one of the
best battle themes in all of gaming this side of Castlevania (slowly builds up before hitting full throttle at 0:40).
Meta-Knight (nearly every Kirby title since Kirby's Adventure)
- Only a "villain" in the sense that he opposes the protagonist. When the "hero" a greedy, shoot-first-ask-questions-later glutton who beats the crap out of you if he so much as
thinks you stole his strawberry shortcake, it takes a sword-wielding masked protector-of-the-peace to put him in his place.
Wolfgang Krauser (Masami Obari version, Fatal Fury II: The New Battle)
- A young, charismatic nobleman just looking for a good fight, and doing a damned fine job of making enemies to get it. Paul Dobson's voicework makes the character just that much more classy ("Joe, once again you are being far too loud. Die quietly, please, or I shall have to ask you to leave.").