Yeah, those choices aren't pure evil. They are just...annoyingly evil. Not the blood-chilling, terrifying, evil villains.
Out of all the games that I've played, I'm going to have to go with those little annoying space invaders from Space Invaders. Especially the last one that's left when you destroy all the other ones. Little thing moves so fast that you have to use the rapid power-up and time your shots correctly. :| Same with the enemy Pong paddle.
As for games with a plot, I'm going with Kefka, from Final Fantasy VI. Most villains want to destroy the world. He succeeded...and became a god-like character. Plus he was an evil clown. Unlike Sephy-chan, who wanted his momma. :B
Of course, Aurapostle's choice of Ganondorf is a popular, and respected, choice.