I'm probably the biggest Ganondorf fanboy you'll ever meet - particularly if we're talking about the Wind Waker version. SO much depth there. I mean, a backstory? In a Zelda game? A GOOD backstory? With MOTIVES!?
Madness.
Speaking of depth and madness, Giygas is a close second. Why? Play EarthBound.
Bowser. He's awesome like that. Now there's a guy who never gives up on a girl, no matter how many times he gets bashed on the head. Same motive from the first game to the last(few extras, but those don't really matter anyways :P), always after Peach.