pikaskipper
Blue Screen Of Death
King dedede. Kirby has been beating him for years on end. Has he had enough?
Tom Nook (Animal Crossing)
Solidus Snake from Metal Gear Solid 2 is one of the best. He could arguably be considered the hero of the game.
Revolver Ocelot is another good one, even if he's not necessarily the main villain. Pretty much any semi-evil character from MGS, really.
The Black Knight from Fire Emblem: Path of Radiance and Fire Emblem: Radiant Dawn. Honestly, I think he's my favorite villain in anything, not just video games.
The guy is not only a badass swordsman (at the time of Path of Radiance, he was probably the strongest human character in all of Tellius), but also a tactical genius and a looming menace for the party for most of the first game. He kills Greil (who we're all shown is pretty much nigh-unbeatable, even despite his crippled arm) without even a scratch, beats Ranulf (who is the strongest Laguz character we've seen in combat up 'till that point) almost effortlessly, and kicks Ike around like a child twice before his eventual 'defeat'. Even then, his boss fight is essentially "I have to get lucky with Aether within the first five turns, or I'm screwed" on Normal difficulty, even with Mist's healing backing Ike up.
Then come Radiant Dawn, it's revealed that not only did the guy let Ike win (and Ike had been shown to be up for the title of "strongest human character" in the series by the time they fought, having kicked the stuffing out of two of Daein's Four Riders and a Dragon Laguz), but he also reveals that he's been dancing on a tightrope for the last god-only-knows-how-many years (at least ten, probably closer to fifteen) playing the part of General Zelgius (Bengion's greatest hero), as well as the Black Knight, without any figuring him out. In addition to that, as Zelgius, he shows himself to be absolutely brilliant (his skill as a commander and his experience even allow him to outmaneuver the tactical genius of Soren), and makes everyone (including the player) think of him as a decent guy and loyal soldier who fights for his country and sovereign with the utmost devotion, while in reality he's essentially the exact opposite (minus the brilliance). He was so skilled that Ike actually thought of him as a teacher and learned a lot just from fighting him, despite the fact that they were mortal enemies.
Honestly, the only thing I don't like about him is that his boss fight in Radiant Dawn is pathetically easy if you give Ike a Hammer before the fight, because the blessing on his armor is gone by then and you no longer have to use Ragnell to damage him. Actually, it's kind of just a letdown in general because he has the Nihil skill, and so your skills won't activate. The only way to make it interesting is to not use Nihil yourself, but that leaves you open to a possible OTK from his Eclipse skill.