Vaati, Legend of Zelda series - Okay, not only is he a Wind Sorcerer, a break from Ganon as a villain, and has been in - I think - three games (couldn't play one, another was easy, and a third I only borrowed from my cuz at the final battle), he was turned bad by the wickedness of the hearts of man. So...he turned evil because he became corrupt by others' influence. Plus, he's pretty cute chibi-fied.
King of Sorrow, Klonoa 2 - Love this guy. Add in the symbolism of who he represents along with what the entirety of Lunatea was about, and you have...a not-so-villainous villain. Really love this guy and to think
Spoiler
Go figure. Gotta love symbolism...Asch the Bloody, Tales of the Abyss - Now anybody who has gone through the game long enough knows his connection to
Spoiler
Since
Spoiler
Quite sad, and the ending.... Gah.
Spoiler
It's just one of those games where if you grow attached enough to the characters, you'll begin to even feel for the villains at times, even slightly. Ignore the following, it just rants on a failed "Tales of" game:
Spoiler
Smithy, Super Mario RPG: Legend of the Seven Stars - What's a great game without a great boss? Even his lair screamed "I'm evil, I'm here, get used to it or I'll have
Spoiler
kill you." Destroying the Star Road, making wishes unable to come true, throwing the world into turmoil, and forcing everyone's favorite star spirit, Geno, to arrive and help out Mario. (Yes, I love Smithy if only for the sole reason of making Geno appear.) Seriously, I mean, you're given clues, you are given a foreshadowed glimpse of
Spoiler
Spoiler
I absolutely love this boss and the satisfactory of seeing "The End" after a tiresome battle (I don't grind). Last time I saw it earlier this year, I immediately wanted to start again. ^_^Oswald the Black Sword, a.k.a. the Shadow Knight, Odin Sphere - If you've never played this, go look it up now. 2D graphics, a wonder soundtrack, and struggling characters all on opposite sides of a war. Well, two wars... The war for the Crystallization Cauldron which
Spoiler
and the war of the heart. Starting off with Gwendolyn and ending with Velvet, Odin Sphere delves deep into everyone's (...okay at least five different someone's) lives as you inevitably face down what has been thrown into motion since the start:
Spoiler
But I digress...a bit. See, Oswald is one of the people that you end up playing as. At first you see him as the enemy, but later on you see just why he was fighting you in the first place. He's a bad guy alright when you start the game, but that's how you were forced into seeing him.
Spoiler
Why is he bad?
Spoiler
Because of that though
Spoiler
I love the plot twists in this game...