Dark Link doesn't really have much of a personality by design - he just stands as a dark reflection of Link, a shadow-being that's often a heck of a nuisance because he mimics all of Link's moves. The weird thing about Dark Link is that it's rarely clear WHAT he is or why he's there. It doesn't seem to be in league with Ganon, or if it even COULD make alliances with anyone. It's just this weird shadow creature that pops up every now and then and presents a different sort of challenge. Most weirdly though is the fact that he serves as the final boss in Zelda II: The Adventure of Link, despite having really no connection to the story.
But if he's truly Link's opposite, he should probably be infused with the Triforce of Cowardice, so those battles should get a lot easier once Nintendo starts responding to my letters.
Not only is Pyramid Head a great and terrifying villain - he's a metaphor for the main character's regret over his actions and his ultimate desire for punishment. But mainly, he's a pretty cool looking bad guy who truly inspires fear whenever there's even a hint of him in the game. What makes it really scary (beyond its entire appearance) is that they're mostly unpredictable - sometimes they don't go after you, sometimes they go after someone or something else, and sometimes they just commit suicide once their purpose has been served. Their entire existence is unsettling and surreal.
Also, they got cool giant knives.
This is definitely the number one villain who's represented by a mask and an ominous moon, probably. I mean, I haven't looked that much further down - but what other villain could also share those qualities?
Anyways, Handsome Jack comes from the GLaDOS class of villains - he's snarky, constantly narrating about your inevitable doom, and berating you at every turn. It helps that he's an unbalanced madman who ALSO happens to be in charge of the largest corporation on the planet, so he has near unlimited resources to try to ruin things for you. His whole presence in the game makes it all the more satisfying once you blast him to oblivion.
Just another classic example of these hippie Vault Hunters standing in the way of big business.
Poor Robotnik - he can't keep a consistent name, he's constantly being belittled by a giant blue rodent, and he just happened to make all of his robots out of the ONE kind of metal that's weak against hedgehog quills. At least he has one of the greatest mustaches in history, although that probably is of little comfort when his gems keep getting stolen by a much of mutant forest critters.
The World of Warcraft isn't the powerhouse it once was, but it's still easily the most profitable MMO going on, and probably the biggest game of the past decade. And the most memorable villain is easily...well, the game itself (destroyer of social lives, conqueror of free time). But in a close 2nd is the Lich King (formerly Arthas Menethil). Sitting atop the mighty frozen throne, he commands the Scourge and stands as a force so evil and twisted, that the Alliance and the Horde lands were united against him. Wielding Frostmourne, the Lich King battle is one of the defining moments in WoW history (right next to the first time you quit and swore you'd never go back, and the fourth time you relapsed).