For me it's Portal.
There is talk going around, based on the lyrics of the opera the turrets sing at the end of Portal 2, that Caroline, the Aperture secretary who was downloaded into a computer and became GlaDOS, was Chell's mom. To which I say: DUH. Of course she is.
Whether or not it's strictly true doesn't matter. GlaDOS isn't just Chell's mom. GlaDOS is EVERYONE'S mom.
She is the parent-as-enemy in the classic hero-quest vein. She's Darth Vader with a guilt trip and strategically placed conveyor belts instead of a fleet and a lightsaber. With all I've sacrificed for you, you won't even come over to the Dark Side just a little? (sighs) Well, I'll just be over here gasping for breath in my respirator egg if you need me.
Parents vs. children is a mythological constant, from what I remember from one of those stunt lectures professors like to give on the last day or two of class, in this case a nifty analysis of the Jungian/Campbellian archetypes in Star Wars. Zeus vs. Kronos, Arthur vs. Mordred, Oedipus of course, etc. - in order for the story to move on (for good or ill), the son must defeat and supplant the father. Even if the father is a good guy, he needs to go in order for the hero to get out from under his shadow and get his personal growth on, which is why Obi-Wan had to die and Gandalf fell off the bridge. But mostly it's a straight-up power clash between the past and the future, between eternal childhood and self-determination.
This is that, but with ladies. Which is rare. Usually if there's mother-figure vs. daughter-figure conflict in pop fiction it's evil-stepmother-style sexual competition. Portal, though... it's part of the first game's awesome simplicity that it's just Chell vs. GlaDOS, with Chell's life/freedom as the stakes and GlaDOS' passive-aggressive megalomania as the driving force. Straight up, no frills. I was actually a little disappointed that they introduced Wheatley and Cave Johnson in game 2; there was something pure and twisted about GlaDOS as a solitary obsessed figure in her claustrophobic, ruined science palace.
But what, you might be asking, makes this story a parent-as-enemy story rather than standard-issue person-vs-insane-computer? Is it that GlaDOS controls Chell's environment? HAL controlled Bowman's environment in 2001, but that didn't make him a parental figure, did it? Nerds, you are going to have to take my word for it, the same way I take the dude's word that the Eyebrow Man's eyebrows in FLCL represent his penis envy: there is just something about the writing that hits me right in the personal myth, and that is GlaDOS' faux-helpful passive aggression.
Yes, men can also aggress passively. I had a really passive-aggressive male boss once - he'd just sit and sigh pitifully and we had to guess what he wanted us to do. But passive aggression is a well-known womanly strategy in which you get to hurt people without losing femininity points for being crass, and most women of my acquaintance do it sometimes, including me (I wish you hadn't made me admit that...) And where did we learn it? From women who came of age when adhering to femininity requirements 24/7 was more expected than it is now, and so much as saying "I am angry" was inconceivable, so it comes out in sweet pleasant language twisted in on itself. Add to that GlaDOS' determination to destroy you if she can't control you, and the fact that the few glimpses you get of the player character are of a young woman, and what does that make?
My psyche, that's what. I don't just have issues, I have an entire editorial staff.
I have to admit, I did like the way the GlaDOS/Chell conflict was resolved - after interacting with Chell as an equal for a while, GlaDOS realizes she can't keep her around as a toy to play with and they part as frenemies. Or at least I have something invested in interpreting it that way.