The whole torn of Curst in Planescape: Torment gets dragged down to Hell by its own wretchedness. You can choose between simply letting its denizens deal with their new problems, or try to redeem them.
Promotional material for Grand Theft Auto V turns the countless cops you'll no doubt gun down into this by implying that the police officers of Los Santos are cartoonishly corrupt, in one case arresting a man for "aggressive filming" and then shooting his dog.
Arguably every pedestrian in Grand Theft Auto V has the potential to become one of these, as the things they say to other people or on their cellphones present them as awful people.
In Assassin's Creed II, at least one gets an Alas, Poor Villain moment: Dante Moro, the brain-damaged bodyguard of Marco Barbarigo. He tries to give Ezio some help with his last words (telling him where the Templars are next). Additionally, after his death you receive a letter from his former wife that he was tricked into annulling his marriage too, stating that she still loves him and hopes for the day that he'll recover and remember her. And, as your informant Shaun tells you, Dante's boss coveted his wife, and so tried to Murder the Hypotenuse. He survived but with severe brain damage, reverting him to a child-like state. This led his boss to manipulating Dante into divorcing his wife and becoming his Dragon. The poor guy was probably the only named victim in any of the AC games you could feel any real sympathy for. Which just adds to potential justification for killing said boss.
In the first Assassin's Creed, there's one mission where you are sent to kill a guy who has been set up as a Torture Technician, who has been kidnapping beggars from various cities, ostensibly to torture them to death for fun. But when you actually track him down, it becomes obvious (to the player, at least) that he's actually NOT evil at all, he's actually a brilliant doctor who is extremely ahead of his time, and he's having mentally ill street-people brought to him because he's trying to cure them with primitive techniques and equipment. Everyone else in the setting is so uneducated and ignorant, including Altair, that they can't understand it and assume he must be lying about wanting to help. On the other hand, it's also implied he's using them as convenient test subjects for the mind control techniques the Templars are having him work on, so he's not completely blameless.
In the Bonfire of the Vanities it is also subverted, some of Savonarola's Lieutenants are pretty forced to do his bidding through the Apple and had no choice in the matter and regret what they have done to Florence in the name of attempting to seek enlightenment or just forced to serve him through the apple.
Finally subverted in Assassin's Creed: Revelations, when after assassinating him on a count of treason, Tarik Barleti reveals that he was executing his own scheme against the Templars, having sold them defunct firearms in an attempt to lure the them out of hiding. Worse yet, Tarik doesn't even blame Ezio for his death, instead blaming his own hubris. Instead of his traditional "Requiscat in pace," Ezio's final words to him are, "I am sorry."
Subverted in Dragon Quest VIII. The Big Bad has been killing people, and you've been following him in the hopes of putting a stop to it. The previous victims have all been high-profile, usually the most important people in their respective towns. Enter Dominico, who clearly is the most important man in Arcadia and seems certain to be the next target. Dominico is also a complete douchebag to everybody in general, but to his servant David in particular, heaping humiliation after humiliation on the doggedly loyal young man, even forcing him to taste for poison in his dog's food. You already know nobody's going to regret this guy's death. Except, it's the eminently likable David who turns out to be the target, rather than Dominico, who isn't quite as important as he thought he was.
The first victim of the supernatural serial killer in Phantasmagoria 2 - A Puzzle of Flesh is the bullying asshole of a coworker at the protagonist's work place, causing Curtis a lot of concern as to whether or not he may have killed him during a psychotic black-out. Then the people he likes start dying, and the otherworldly antagonist gets a lot less subtle.
Ironically, this winds getting such a massive case of Alas, Poor Scrappy it winds getting subverted, especially because his replacement is such a shameless, spiteful whore that even the teenage guys who hated the first person hate the successor MORE because she manages to outdo the Asshole Victim she replaced in being a Jerk Ass, and this is so bad it overpowers any of her Ms. Fanservice tendencies. And, considering how ass ugly (in temperament and appearance) who she replaced was, that is quite a feat.
In Knights of the Old Republic, the player character gets the chance to solve a murder. Turns out the victim was having an affair with one suspect's wife, and had been in a fight over business with the other suspect.
Later in the game, the PC gets to do play detective/lawyer again, but this time the trope is completely inverted: though the victim is a Dark Jedi — and as such, no girl scout — her murderer is even worse. And infuriatingly vital for the Republic's war effort.
The game does not force you into saving the murderer, however.
Almost everyone of Agent 47's targets in the Hitman series is some kind of big-time criminal. Sex traffickers, mobsters, terrorists, and corrupt politicians are just some of 47's victims. However in cutscenes, 47 has murdered a presumably innocent postman to protect his identity, and Requiem in Blood Money has him kill a priest and reporter to protect his identity. In terms of targets, stand out "innocents" are the failed private investigator in that biker level. Completely innocent targets are still in the minority by a great margin.
Condemned: Criminal Origins, All the victims of Serial Killer X/Leland were all serial killers themselves. He would kill them the way they killed their victims. Needless to say all the murders were fairly brutal.
Playing with this trope: in Oblivion on the Dark Brotherhood quests, about halfway through the questline your anonymous orders stop being 'kill this person, no reason given', and start painting a detailed picture of the asshole you are about to murder. They are all lies, but the victims really did kind of have it coming - you have been unknowingly bumping off the leaders of the Dark Brotherhood itself.
First few are still assholes. You've got a pirate, a rapist, a guy who had the Brotherhood kill his own mother to save his skin (unfortunately he lives if you finish it "right"), a warlord, that mouthy dark elf from the tutorial, and a mooching drug addict. The only person on the list of slaughter victims who wasn't a jerkass of one stripe or the other was Baenlin.
In Skyrim: the first target for the Dark Brotherhood assassin's guild is an orphanage matron by the name of Grelod the Kind, who is anything but what her name implies, and is quite the cruel Child Hater. When you first enter the orphanage, you find her threatening to give the kids of the orphanage an extra beating if they don't step up their chores, telling them they're her slaves until they come of age and she can kick them out, and that if they think of escaping like Aretino (the orphan who called the hit on her) she'll make them suffer for it. She then ends off by making the children force themselves to say that they love her. If you forgo silence and just decide to kill her in view of the orphans, they cheer.
And then the initiation ritual has you kill a barbarian with a hidden Blood Knight streak, a feisty and crass woman who has murdered people with her foul words and temper and a Khajit (Thief, murderer and rapist) who expects this to be his death. With a broader definition of "asshole", you can also kill the Dark Brotherhood assassin who brought you there.
Another Brotherhood target, Clan Shatter-shield, is also rather unsympathetic, though this is only seen in quests outside of the Dark Brotherhood questline. They turn out to be a family of Corrupt Corporate Executives who treat their foreign workers like garbage and sic pirates on their competitors.
Nearly all of the people the Thieves Guild sends you after are this. Examples including an oppressive, penny pinching beekeeper, a slave driving meadery owner, an Argonian con artist, and the man who betrayed and murdered the original guildmaster. Though in the case of the Con Artist, he just agrees to work with Guild and becomes a fence for you.
In Mass Effect 2, Thane's loyalty quest goes to great lengths to show that the target of Kolyat's assassination attempt is corrupt. Even in the outcomes where he winds up dead (including by Renegade Shepard's own hand), everyone cares more about what's going to happen to Kolyat; you can even talk the C-Sec officer into not pressing charges for attempted murder. Thane's role as The Atoner involves specifically targeting these. In fact, you meet him during what was to be his last job, a Corrupt Corporate ExecutiveBad Boss.
In Mass Effect 3, the Batarian Hegemony is a xenophobic, insular, isolationist society that practices slavery, regularly condones acts of terrorism against the Council races, and is gearing up for war with the Alliance. It also happens that the Reapers invade the galaxy through batarian space, and the Hegemony folds like a house of cards. Unfortunately, this all hurts the many decent batarians who had no control over their government.
Also in Mass Effect 3, Henry Lawson, Miranda Lawson's father, had already been described by Miranda as a narcissistic abusive father who wanted to control every aspect of Miranda and her sister, Oriana's, lives (even making Miranda unable to conceive children). Then it turns out he's even worse, as he sets up a facility masquerading as a refugee camp for displaced families and those with family members fighting in the Reaper War to come and stay. Unfortunately, everyone who goes there is either indoctrinated into a Cerberus agent, converted into husks to study the Reapers, or murdered and experimented on, with him overseeing the deaths of thousands or millions of people. While normally a morally ambiguous act, when Miranda biotically throws him out of a window to his death after he lets go his hostage (and other daughter, Oriana), it's safe to say no tears were shed.
Killing both Mr. Burke and Allistair Tenpenny from Fallout 3 yield good karma from killing them, and there are other such friendly NPC's who have crossed the Moral Event Horizon enough to get this.
In Fallout, pre-war America in general was this. Bearing little resemblance to the real life United States, Fallout-verse America was a jingoistic, genocidal, dog-eat-dog state that thought nothing of violently annexing Canada, stomping out individual thought and rounding up dissidents to put into concentration camps and use in horrific social and medical experiments, all behind a thin veneer of 1950's suburban utopia. It has to be said that as bad as the irradiated, mutant-infested post-apocalyptic wasteland is, it's actually an improvement.
Ragou and Cumore in Tales of Vesperia take this trope Up to Eleven. In the first act of the game, Ragou is found to have been feeding some of the already-abused citizens of the town he governs to monsters for entertainment, claiming that the party doesn't understand the high class of taste it takes to find it amusing. Watching him walk away the first time he is caught is one of the most difficult parts of the game to sit through. In the second act, Cumore has been forcing citizens of the desert town he has jurisdiction over to search for an ancient and powerful phoenix-like creature. They are dropped in the middle of said desert to search for said monster. Assuming they found the monster (no one does), it is more than capable of instantly killing anything, including similar god-like creatures. When both are finally brought to justice, the legal system of Terca Lumireis lets both of them go with either a minor reduction in rank or no punishment at all. Both assholes meet their end — Ragou is slashed across his back and dumped into a river; Cumore is backed into what is essentially a pit of quicksand — at the hands of disgruntled Imperial soldier turned vigilante Yuri Lowell... whose reward is to get ragged on it by his borderline Lawful Stupid friend and ex-comrade Flynn Scifo.
While the player commits many atrocities in the Death Knight starting quests in World of Warcraft, often against civilians, the primary opponents are the Scarlet Crusade, which tortures and kills perceived enemies, and whose leadership leaves many of the civilians to die in order to flee and attack the Scourge in Northrend. The Lich King's forces may still be worse, but the Scarlet Crusade is also considered an enemy by the other groups fighting the Lich King because of their extremist positions.
By "perceived enemies," they mean "anybody who might be corrupted by the Scourge." And by "anybody who might be corrupted by the Scourge," they mean "anybody who isn't part of the Scarlet Crusade."
Also in Warcraft III, you probably still cheer when Garithos is killed by Varimathras and devoured by ghouls.
In Mount Hyjal, your character infiltrates the Twilight's Hammer to conduct sabotage. To prove your loyalty, you have are ordered to execute some of the failed applicants who are held in detention. Luckily for you, the Twilight's Hammer functions on Klingon Promotion and every single prisoner is more than happy to attack you and offer your blood as a sacrifice to the Old Gods.
In Freespace, we learn through an Apocalyptic Log that the Shivans killed off a species of Precursors (the Ancients) 8,000 years prior to the game. This log, written by the Ancients, paints them as victims of horrific destruction at the hands of the Shivans. It also, however, chronicles the rise of their empire, during which they met other advanced life, "And we subdued it, or we crushed it." In other words, the Ancients traveled around the galaxy enslaving and annihilating other species to expand their own powerbase. It's kinda hard to see the Shivans as the bad guys during that conflict.
The fan project Ancient-Shivan War, which covers this area of Freespace's history, portrays the Ancients as a very stuck-up warrior culture who consider all other forms of life automatically inferior and who glory in the genocide of a less advanced species early in the game. Fans are somewhat mollified by knowing exactly what's goingto happen to the Ancients in later installments.
Then there's Benny the guy who shot the courier and buried him/her. He dies either in two ways. One you hunt him down for Mr. House. Or he is captured by Caesar and you get to choose how to kill him.
The Great Khans tribe qualifies as well. On the one hand, a rather severe foul-up on the NCR's part led to a massacre that saw the Khans getting absolutely devastated; years later they still haven't recovered. On the other hand, the Khans were openly hostile to the NCR long before the event in question, and not terribly nice even amongst each other. Their leader outright brags about how they laid ruin to defenseless NCR settlements, and a former Khan that later defected to the NCR will angrily comment that the group got exactly what was coming to them.
In Heavy Rain, at one point the story hits this point. Ethan is forced to go kill a man in order to find a clue to his son. The victim is a drug dealer who chases Ethan around the apartment with a shotgun until they reach the daughters room and the victim runs out of ammo. To make the choice a difficult one however, at the last minute he reveals he has two daughters and begs Ethan not to shoot, however he has already chased Ethan around like a jerk and revealed his occupation. To be fair, even if the guy catches Ethan, he lets him go without attacking him anymore, and considering Ethan pulls a gun first, that certainly bumps him up on the nice list.
The same happens to the owner of the Blue Lagoon who turns out to be a pervert and a rapist, but is shot by the Origami Killer.
Lt. Blake has become this in two ways: the "Uploaded" ending where it is implied he'll suffer the effects of the ARI. Or than being suspended for Ethan's death.
The comment under Table Top Games for "dungeons" applies to numerous video games as well. For example, in The Elder Scrolls series, if you see a small cavern complex, you can rest assured that at least nine times in ten it will be full of Necromancers of Conjurers or the undead or other perfectly acceptable targets you may ruthlessly cut down without a single ding to the Karma Meter. You can then with no guilt grab everything in the place and haul it back to the nearest marketplace. The remaining one time in ten you will speak with the inhabitants. Half the time, you will put them all to the sword because someone told you to, then take their stuff and sell it.
In Fire Emblem: the Binding Blade, it's related that Big Bad Zephiel's descent into villainy began when he strangled to death his father Desmond, who had had at least two hits put out on his son prior.
In Dishonored everybody on Corvo's hit list is part of this troupe. The tagline of "Revenge Solves Everything" should have been the first clue.
In The Walking Dead game, had a town called Crawford where everyone in it were turned into Walkers. The town itself is run like the Khmer Rouge, where they kill people they deem a burden to them, children, the elderly, and sick. Some of the survivors considered that the people in it got what they deserved.
All of Anaksha's targets in her games qualify for this trope, the horrible things they do to people qualifying them for death by her sniper rifle.
In the Goblin quest series in RuneScape, the first thing Bandos does after he commandeers Zanik's body is make her execute Sigmund. We're supposed to take this as a sign that Zanik is Not Herself, but given that Sigmund had attempted genocide of the Goblin race, which Zanik is a member of and Bandos is the patron of, three times at that point, few players were sad to see him go.
Final Fantasy IX: Lampshaded by Vivi, who states (in narration) "I hated Brahne. I wanted this to happen to her." However, it's subverted second later, when he laments "But then I saw Garnet cry...".
In Homeworld you capture one of the frigates responsible for the destruction of your civilization. The captain is interrogated for information on why this happened, which he reveals. It is clinically noted that "the subject did not survive interrogation".
In Suikoden, any time you have elves in the game, you will have on average two who aren't complete unrepentant assholes. In the first game, their general dickery bites them on the ass in a big way - the elven home tree is a gigantic target for the Burning Mirror at Kwanda Rosman's fortress, which has a straight shot at it. One of Rosman's lieutenants, Valeria, goes to the elves to try to warn them. She speaks to them for all of fifteen seconds before they begin hurling speciesist insults at her, then throw her in the dungeon. When you return from the (similarly dickish) dwarven lands with a weapon that can neutralize the Burning Mirror, you can see the elven tree on fire in the distance. The characters in the scene are shocked and horrified, but most players can't help but smile a little inside (doubly so because all of the not-asshole elves survive).
Resident Evil 6 has one in the Leon/Helena campaign. One of the Tall Oaks gun store survivors is a sociopathic survival-focused Bastard BoyfriendC-List Fodder who spends his whole screen-time verbally abusing his girlfriend and complaining that she's slowing him down and should be left to the zombies. Helenaespecially calls him out on this, understandable given her personal past experiences. Eventually, Peter decides that he'd have a better chance of survival if he went his own way, so he forcibly takes his girlfriend's gun and runs out the gun store, where he is promptly eaten by a zombie. The only person who feels even remotely upset is his now ex-girlfriend.
However, given the nature of Shadowrun you don't know this unless you go through sparing him. Even if you decided to put a bullet between his eyes later, the employer is furious at you for knowing too much.
Subverted completely in Payday 2 with The Elephant, Big Oil and Election Day have you targeting innocent politicians and scientists for once.