1. Kefka from Final Fantasy VI. He succeeded where most the overrated pretty ever Sephiroth failed miserably. He actually destroyed the earth and ruled uncontested for a long time before being defeated, and this is DURING that game's present story, not just the prologue.
2. Ganondorf from Zelda. He is the Joker and Lex Luthor of the gaming world. What can be said?
3. The Ancients from Eternal Darkness: Sanity's Requiem: Ulyaoth, Xel'lotath, and Chattur'gha. Why? Because they're all like Cthulhu. They are Elder beings of pure power that are trying to escape their present confinement in order to destroy then reshape the world. The only way to defeat to them? Play them against each other. You don't have a chance any other way they're so badass.
4. Lord Yggdradill from Tales of Symphonia. The heroes aren't trying to stop him from conquering the world. He's already done it. He's already ruled uncontested for 4,000 years without anyone even knowing it. He just keeps manipulating the world using the false, but dominant, the religion he created to perpetuate an endless cycle of violence and droughts, off-set by periods of prosperity, only to have the violence and generation long droughts start up again after certain conditions are met.
5. King Bowser from Super Mario Bros. Yeah, yeah, he's a bit of a butt of a lot of jokes now, but back when I was a kid he was a genuinly menacing villain, and the first villainous icon in gaming ever. He's earned his way onto my list if only because of the historical value he has concerning game villains.
6. Dracula from Castlevania. Because he's frikkin Dracula. You couldn't make him lame or non-badass if you tried.
7. Dr. Robotnik from Sonic. The only villain in a Green Aesop not to be annoying, but actually seem like a genuin threat. He gets huge points for that alone. The Captain Planet villains should take a lesson or two (or three) from him.
8. Ghaleon from Lunar: The Silver Star. He usurped the throne of a frikkin god and then took his revenge out on the whole world by utterly obliberating all the water and fertile before being defeated. Why? Because he thought that the god he once worshipped let a friend of his die despite his prayers and pleas. Its not a great motive, but it sure was nice to see a personally motivated villain for once.
9. The Germans in any game about WWII. Enough said.
10. Any of the primary villains from Final Fantasy XII. Okay, not the best FF title, but once you know what's going on, you realize that the villains reach such levels that they're definitely magnificant in their bastardry.