Kraze Miles from Suikoden I is my first thought. Dude is such an evil little shit karma Houdini, then you get to execute him. And he's literally the only NPC in the entire game where you're given that choice and actually doing it has no effect on the good ending. Because yeah, fuck him!
Shanath in Baten Kaitos Origins is another major one, even if they tried to make him slightly sympathetic at the very end. Dude frames you for assassinating the emperor, causes you trouble and wrecks you throughout the game, rips your mom's wings out of her back, and is the most condescending smug prick about it all the entire time. It felt SO GOOD to finally kick his ass!
Any Samurai Warriors game where you can actually kill Ieyasu Tokugawa is greatly appreciated, too. They almost never let you kill him, and other games based on the Sengoku period pretty much never do or make his side the protagonists.
Luca Blight from Suikoden II and Algus from FFT are also great examples.