Eve, Parasite Eve
A quivering, goopy humanoid composite of microscopic creatures straddles the Statue of Liberty and gives birth to a genocidal scourge. This boss fight definitely has the highest gross-out factor of any on this list, so if that’s not your kind of thing, you might want to steer clear of the following clip:
Either those mitochondria have nothing but contempt for the human form, or they just don’t know what it should look like from the outside. Why does Eve have hands growing out of her head? Why, if the mitochondria hate humanity with such a passion, do they then craft their ultimate warrior to resemble a woman? Eve won’t answer any of these questions, but she will wax poetic about the shortcomings of humanity and try to claw poor Aya Brea’s heart out of her chest.
 The Boss, Metal Gear Solid series
She’s the original mullet. The protomullet, you might say. The mullet to rule all other mullets. Both a mother and a killer, the Boss is deliciously complex. When she juxtaposes the revelation of her terminated pregnancy to a pain metaphor that shames and demoralizes the protagonist, The Boss tugs at the emotions of both the player and the character through which he or she experiences the game.
With its eye-catching drifts of flower petals and unsubtle blood imagery, the fight against The Boss might be a bit over the top for some tastes, but I find it moving just the same. Props to the development team for working realistic combat camouflage into the game mechanics; The Boss blends perfectly into her surroundings and makes puts up quite a fight.
 Queen of Blades, Starcraft 2: Wings of Liberty
I’m not sure what disturbs me more, the Queen of Blades’ demonic appearance or her resemblance to the woman she derives from. You don’t have to look terribly close in this video to see that the Queen retains some of Kerrigan’s mannerisms and expressions, and I find the effect incredibly eerie.
Combining the raw ferocity and regenerative capacity of the Zerg with the psychic finesse of a Terran scout, the Queen is one of the most terrifying video game combatants ever animated. She embraces a fatalistic viewpoint that makes a poignant counter to Zeratul’s cautiously hopeful outlook, particularly in light of the betrayals and pain that make her who and what she is.
 Persona 4: Izanami
This pick is a massive spoiler. If you’re planning a Max Social Links playthrough of Persona 4: The Golden on your Vita and prefer to avoid any hints of what’s to come, please don’t read on.
It’s entirely possible to play Persona 4 from beginning to end without ever encountering a hint of Izanami’s existence, but arguably she’s responsible for each and every conflict in the game from start to finish. She’s just so subversive and sneaky about it that you don’t even know she’s there.
If you’ve played the game before, you may recognize her as the seemingly innocuous gas station attendant who approaches the protagonist at the beginning of the narrative. She’s the puppet master behind Adachi and Namatame and the architect of the trials the protagonist faces while visiting the world of the Midnight Channel, all without anyone—even the player—ever realizing what was really going on.
The epitome of the villain every player loves to hate. No other nemesis since Moriarty has gotten so diabolically under my skin, and Moriarty didn’t sing, so who wins that contest? I wanted to strangle GLaDOS the first time I heard her voice, and that sentiment pretty much carried me through to the end of the game.
Was it healthy for me to grind my teeth every time GLaDOS taunted poor Chell (and by extension, me)? Probably not. Was I happier than I should have been when I sent the cantankerous she-bot into catastrophic shutdown? Definitely. Most importantly though, GLaDOS takes the gold here because in many ways, she’s gameplay. She’s the carrot and the stick; her commentary is both reward and punishment for finishing a puzzle.
The other villains in this list are like movie villains: they swoop into the narrative, say their lines, and then swoop back into the shadows. GLaDOS don’t need no stinkin’ shadows. She’s there every moment of the game, a relentless agitating force driving the player ever onward.
There were many other candidates who didn’t quite make the cut. From Dragon Age’s Broodmother to System Shock’s SHODAN, they all had their distinctive styles of evil-doing, but in the end I had to pick just ten.
If you disagree with my choices (how dare you?!), please drop a comment to let me know. I’m always happy to enjoy a friendly greatest-thing-ever debate.