Here are the main reason: beautiful, smart, poetic, powerful and he became much more then he was suposed to.
(Zidane was suposed to be MUCH stronger then Kuja but Kuja power is just to much for Zidane.)
Ghaleon, from the Lunar series on Playstation. He had tons of character, motive, and was just plain old badass.
He definitely ranks up there.
As for favourite game villain, I'd say SHODAN from the System Shock games. Cold, merciless and cunning, she was an almost unstoppable machine and the best part is that she was always manipulating you to do her bidding, whether you knew it or not.
Sephiroth, but for the sake of origianality i'll go with Tyrant/Nemisis from the RE series. When he dropped through the roof in RE2 I nearly pissed myself.
Twenty-eight days... six hours... forty-two minutes... twelve seconds. That, is when the world will end.
Sephiroth, because he's one of the most twisted individuals out there, not to mention he has a kickass sword and can incinerate towns and take pleasure in it.
Oh, the villain in Max Payne 2 was interesting as well, as the storyline made you hate him, yet accept his motives at times. It was just strange altogether.
"Stephen Wolfram is the creator of Mathematica and is widely regarded as the most important innovator in scientific and technical computing today." - Stephen Wolfram
For my style of thinking, there hasn't been a videogame villain that I am truly satisfied with let alone one I consider my favorite. I'm just waiting for videogames to accept darker themes.
For now I'll have to go with Kain, because he has no mercy.
The main problem I find with most game villains is that they have no understandable motivations for their actions. I actually like villains I can sympathise with and heros who are close to being villains themselves.