2) "Detonation code activated" (Metal Gear Solid)
So get this: after trekking through a labyrinthine nuclear waste facility in Alaska filled with genetically-engineered test tube soldiers, psychics, wolves, and a whole lot of cracks in the fourth wall, hero Solid Snake has to activate a special card, which will only work after being shaped by extreme temperatures, to stop the terrorists. Only, as Snake finishes up this extremely boring and time-consuming task, he receives a call from his clone twin brother who reveals that he's been guiding the poor sap since the beginning while in the guise of his old mentor. Oh, and instead of deactivating it, Snake just armed the giant nuclear robot dinosaur. Good job, buddy. But hey, if that's not your favorite twist, don't worry. There's like twenty more in there.
1) Welcome to the Dark Side (Knights of the Old Republic)
The twist. The motherload. The one that was on everyone's mind and whispered among gaming faithful in dark alleys, mini-malls and snack shops. That prick who sorta started the whole Sith vs. Old Republic thing that screwed over most of the galaxy? The nefarious and conspicuously-masked Darth Revan? Well I hate to break it to you, but it turns out you were that evil overlord the whole time. And who knew but didn't tell? Why, that innocent-looking pig-tailed hottie over there. She lied to you. Sure there were twists before KOTOR, but BioWare cemented their place as tricksy hobbitses with this one. Their success helped usher in an era of plot-heavy gaming that demanded to be taken seriously. Even if your only companion ended up being the homicidal assassin droid. Tearful response: I love you too, meat bag.
Honorable Mention: Samus is a GIRL? Say whaaaaaaaat? (Metroid)
Yes, okay, I freaking get it. Congratulations, you were shocked that the digital representation of a fictional character could have tits and still murder space pirates. The only reason this is a twist is because the misogynist assumption at the time could be summarized as Girls + Videogames = World-Ending Paradox. Oddly though, this thought process still lingers in some dark corners of gaming. How very odd.