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Nazis - as seen in quite literally everything ever, except in Germany
By sheer weight of numbers, these have to constitute the number one villain in videogames. No one likes Nazis, therefore they can be murdered in absolutely massive numbers with almost no fear of someone complaining. If games didn’t have a specific group of real people so unarguably intertwined with evil, where would we be now? 

Nihilanth - as seen in Half-Life
The Boss of Xen sticks in the mind not just because he looks like a baby suffering from elephantiasis, but because he’s so tragic. Look at that big, sad potato face, then peer closely and you’ll see manacles on his skinny wrists. Even before Half-Life 2 revealed a third party, the Combine, as being architects of the first game’s invasion, it seemed the forces of Xen were attacking Earth against their will. Busting the big guy’s head open and shooting his brains seems a horrific crime once you realize that.

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Onyxia - as seen in World of Warcraft
Lo, how the mighty, etc. Formerly one of World of Warcraft’s toughest raid opponents, requiring 40 men to take her down, now the broodmother of the Black Dragonflight has reportedly been given what-for by less than five level-70 Burning Crusade players. She’s deeply entwined in ongoing Warcraft lore (there are rumors that her daddy, Deathwing, might eventually show up too), and can even be found concealed in a human disguise standing serenely next to the boy-king of Stormwind City.