Dr Neo cortex: crash bandicoot series. He's funny and Clancy Brown's voice was so good for him.
Ganondorf: windwaker. This version just has a bit more backstory and feels more fleshed out.
Hades: kid icarus uprising. They did such a good job hiding him the build up to this game. None of the levels from after you beat medusa were used during the advertising of this game. He is the funniest video game character ever while also being extremely intimidating and evil.