Remember Me (Changing people's memories and destroying their lives)
The jury's still out on Remember Me. An interesting premise with some flawed mechanics, a vibrant world we can't really explore, Capcom difficulty with in-another-castle reward. But when it comes to the game's morals, things are a little more certain: in changing memories, you are ruining lives at every turn. Good work there.
It's not always obvious that this is going on, since some of the people whose memories you alter turn out better for it. Then there's folks like the bounty hunter you meet early in the game, who wants to bring the protagonist in because the reward will pay for an important medical procedure for her husband. You have no choice (literally--the game forces this one) but to go in and change her memories so that she thinks her husband recently died, and she becomes your trusted ally to get back at the hospital. Keep in mind that he is actually still alive, but probably not for much longer, and you never tell her what you did. Wow, some friend you are.
Grand Theft Auto (Unnecessarily gruesome punishments)
Grand Theft Auto is the sort of game you turn off your guilt-o-meter before playing. A series where you hijack cars, run down innocent civilians, and commit insane and deadly stunts just to progress (oh, and kill hookers, can't forget about that), you're probably going to drop the controller in the first five minutes if you're prone to remorse. However, some parts of GTA are even hard for veterans to handle, and unfortunately, they're not always the sort you can avoid.
The torture scene from GTA 5 comes to mind: Mr. K is willing to just tell you what you want to know, but Steve goes by the logic that "duress is best, giving Trevor free reign to be a psycho and forcing the player to go along. Maybe we didn't want to waterboard the guy after ripping out his tooth and beating him with a wrench, but that isn't our call to make. While it wouldn't make sense for Trevor to be too soft-hearted, one can't help but feel gross for torturing a man who is literally begging to cooperate.
BioShock (Killing the Big Daddies)
Oh, the Little Sisters--nothing like looking at a little girl and deciding, naw, she's lived long enough. Players from all walks of gamedom tell of the shame they felt after killing a Little Sister, but at least there's a choice in that regard. There's another Bioshock enemy that, in the end, you will kill if you're going to survive, and feel like a jerk for it: the Big Daddy.
The results of horrible experiments, the Big Daddies are conditioned to protect their Little Sisters no matter what. Over time they seem to grow genuinely attached to the girls, banging viciously on vents and even crying when they can't be found. Unfortunately, you need the ADAM from that child, and without it, you're not going to be able to beat the game. So you have to kill the Big Daddies, who just want to protect their girls, and they die knowing that their Little Sister is a goner without them. It's suddenly not so great being the thing that goes bump in the night.
Portal (Euthanizing the Companion Cube)
There's a certain exhilaration to completing Chamber 17 in Portal--you've not only overcome the game's most mind-bending puzzle yet, but in this void of human interaction, you've made a new friend. That's what makes GLaDOS' comment that the Companion Cube "cannot accompany you for the rest of the test and, unfortunately, must be euthanized" one of the most devastating lines ever.
Oh, we tried to think of a way out. We propped the box against the side door, tried to knock down the camera as a sacrifice to the flaming maw, even stood there and waited to see if GLaDOS would look the other way just this once. But it was all in vain, because if there's one thing GLaDOS loves, it's subjecting Chell to psychological torment just to see what she'll do. Or maybe that's Valve--they did have that line about destroyed turrets' simulated pain being "real enough for them", and all those dead-end hints about Half Life 3...
Shadow of the Colossus (Everything)
Admit it: you knew this was going to be here. Shadow of the Colossus is equal parts beautiful art, clever puzzles, and thought experiment. While Wander's mission is noble and we as players want to help him succeed, it's hard to ignore the twinge you get when a colossus screams and reels in pain as you kill it. It gets a little easier as the game progresses, with the colossi getting scarier and more aggressive over time (as opposed to colossus number two, who's like a puppy trying to follow you home), but even then it's hard to justify.
Thing is, at their most vicious, they're just territorial animals, and there's no threat that they're going to burn down your village or kill your loved ones. This isn't slaying Smaug so that he doesn't destroy Laketown--it's tossing thermal detonators into the Sarlacc pit for funsies. That's something the game wants you to understand. It makes you seek the colossi out, sometimes chase them down, and witness the pain your violence causes--and the whole time it asks, why are you okay with this? The fact that your actions have disastrous consequences almost isn't necessary. You know what you've done.
The Last of Us (Joel's final decision)
SPOILERS AHEAD for The Last of Us. Naughty Dog's latest isn't intended to provide a branching, choice-driven storyline. Its a resolutely linear, resoundingly affecting tale of survival and responsibility that, while entirely on-rails, does do a great job of making you feel burdened with the weight of your increasingly brutal actions. Throughout the course of the story, theres a subtle, almost ambient sense of guilt about the kind of experiences you're putting Ellie through, and the kind of things shes having to do, in the name of keeping you both alive.
That is, until the end. With Ellie anesthetized and unwittingly ready for a fatal brain surgery that might well save all of mankind, Joel snaps. Having lost one daughter already, he decides that saving Ellie is more important than saving everyone else, and busts her out in a roaring rampage of bloodshed. Theres no moral choice here. Joel has made the decision for Ellie and the player. While the lack of branching ending possibilities annoyed many, its also a brave move, subverting traditional video game heroism in favor of a more real, more flawed, reality. But still, you've doomed mankind to indefinite suffering. And you didn't get any other option.