3. Golbez (Final Fantasy IV)
Even though this towering knight is upstaged at the end of the game, you'll hate Golbez's guts from the moment he sets foot on the screen. He's a manipulator, a liar and a mind controller, all things that serve to hinder your progress throughout the game. Golbez affects almost every character in the game on a personal level, either by taking something precious by force or actively killing characters in cold blood. Late in the game astounding revelations are made about his origins, and the twist makes this character even more interesting. Golbez may not destroy the world, but in 20 short hours he manages to wreck the personal lives of your entire group. Damn.
2. Sin (Final Fantasy X)
It's hard to give such prominent placement to a giant ... whale monster thing... but once the credits roll in FFX you'll understand exactly why the mysterious, destructive monster known as Sin ranks so high. What initially seems like a mindless monster with no purpose other than to randomly terrorize the world opens up one of the most mind-ripping plot twists we've ever seen. The creature is an indestructible enigma throughout the entire quest, and only when you brace for the final stretch do you realize the terrible truth about Sin and the world of Spira. That's some heavy stuff. In the end, Sin is a total mindjob, from creepy introduction to blazing finale. And the ending... that must be the most satisfying high five in the history of RPGs.