Heh. I just stumbled across this randomly, having had no idea it had ever gone online - a pop piece I wrote for PC Gamer last March on PC gaming's finest villains. Well, the finest that fit easily within an A-Z list, anyway. No, your favourite villain is not in there, and yes, shame on me for the oversight. How dare I call myself a PC gamer, etc. Why don't you mention him/her/it/them/[no suitable pronoun in the English language] below instead?
Here's a couple of random entries:
Ethereals - as seen in UFO: Enemy Unknown
The first X-COM did a splendid job of cleverly regurgitating sci-fi tropes to create its alien races, but these creepy, floating robes turned up late in the game and shook our faith in our own abilities. Unnervingly resistant to conventional weaponry and largely attacking with psychic powers rather than the guns of other races, they were the silent masterminds of the alien invasion of Earth. When you finally managed to capture one and dissect it for research, it turned out that, underneath the Jawa chic, it was a spindly pink thing a schoolboy could rough up.
The Pope - as seen in Medieval: Total War I and II
Calm down, Catholics - no matter how much he might look like Emperor Palpatine, we’re not calling the current Pope a villain. In Medieval, however, he’s a colossal pain in the behind. Consistently spoiling your fun (if France can’t be invaded, then what’s it there for?), he makes petulant demands of his own, then punishes you if you can’t meet them in the stingy amount of time allotted. He’s often your single greatest impediment to building a mighty empire. Revenge can be had in Medieval II, where you can kill or kidnap him and a new, similarly vulnerable Pope soon pops up - enabling mass papacide in the space of just of a few turns. It’s an angry atheist’s dream.