Knights of the Old Republic: Near the end of the game, after crossing the point of no return, you can decide once and for all if you are good or evil. Pick evil, and your fourteen-year-old Playful Hacker ally Mission will try to fight you. Her Wookiee pal Zaalbar will normally side with her, but you can call on the life debt he owes to youand force him to kill her. If you bring him along when you storm the Star Forge, he will turn on you, but by that point you're probably powerful enough to dispatch him easily.
Lisa Garland in Silent Hill 1. In the Good endings, she kills Kaufmann, who turned her into a drug addict and (possibly) killed her before, either directly or as a result of her addiction. It's likely that she took more offense on the latter one. Though the Lisa in the game isn't the real Lisa, just a construct controlled by Alessa, and Kaufman helped the cult do far, far worse things to her.
Subverted in Jagged Alliance 2. You'd think Eliot, the poor bastard that's been beaten up by the Queen the entire game, would be more sympathetic to the mercenaries that are about to kill the sadistic bitch. Not so much. In fact, if you take too long to get to the palace, you can't even bypass him: you have to kill him.
Played straight with the Warden's husband though; although thinking about it, his dialogue suggests he's pissed off from having to look after the kids all day while his spouse works...and so he'll happily HELP THE HEAVILY-ARMED SOCIOPATHS, WHO JUST BROKE INTO HIS HOUSE, KILL THE SOLE BREAD-WINNER. Unfortunate Implications, indeed. (But then, she is a prison warden, so fuck knows which end of this ass-backwards relationship is more to blame here)
In Clive Barker's Jericho, the Firstborn is attacked and killed (presumably, it is never made clear) by Arnold Leach after the latter realizes that he was nothing more than the Firstborn's pawn.
There's a difficult-to-properly-understand scene in the end of Twilight Princess that implies that Ganondorf was betrayed by the new villain, Zant, who he had been using as a conduit. As Ganondorf struggles to maintain his willpower, and reaches deep within himself for new strength, we see a shot of Zant. Zant snaps his head to the side, as if cracking his neck, and Ganondorf dies. Maybe for the last time.
Except that by all appearances Ganondorf didn't abuse Zant, and kept both the letter and spirit of his promise, as Zant was indeed made the Twilight King (and worshiped Ganon as a god). A better example might be Midna going medieval on Zant after his defeat; this might also explain the above scheme seeing how Ganon's power was the only thing keeping Zant alive at that point.
They were brainwashed, actually. Darion Morgraine, commander of the Ebon forces, snapped out of it when the ghost of his father rose from the chapel they had just failed at assaulting. While it's not shown in the game, the Death Knight graphic novel implies that all of the Ebon Knights (or at least the ones that didn't return to the Scourge) had a similiar encounter with their own dead parents. So a better question would actually be: Was it really a good idea to play the We Have Reserves game on your elite forces on the holy ground where their ancestors rest?
In the Halfus Wyrmbreaker encounter, players must free the enslaved drakes around the arena, who put a debuff on Halfus that prevents him from using his abilities as effectively (for example, one reduces the amount of damage Halfus' proto-drake does, while another enables tanks to get an occasional reprieve to clear their debuff stacks). They are mind controlled and must be killed afterward, but killing them puts a damage-increasing debuff on Halfus.
Do NOT attack followers, or any friendlies in Fallout 3. Even Dogmeat bites back.
Viking: Battle for Asgard: Done literally when Skarin unleashes Fenrir because Freya broke her promise to let Skarin seek entry to Valhalla after killing Hel.
During the climax of Final Fantasy XII, Vayne boasts his own power and makes not-so-veiled threats against his brother, Larsa. Just as the heroes confront him, who would chance to overhear but Judge Magister Gabranth, charged with Larsa's well-being by the late Emperor Gramis, and whom Vayne had treated as nothing more than a hound and a blade to further his own political ascent.
Arguably, this was part of Vayne's plan, Magnificent Bastard that he is. The threat on Larsa at least; earlier cut scenes strongly implied that even with his fratricidal and patricidal history, Larsa was the key to his plan in the end (forge an empire with a bloody war and underhanded tactics, cross the Moral Event Horizon a few times, and leave everything to his young idealist brother who would emerge with clean hands from it all). Vayne's treatment of Gabranth was likely just the way he was, an arrogant jerk.
In Arcanum: Of Steamworks & Magick Obscura, the player can find several half-ogres magically bound to a cruel master in the Dark Elf village. Killing this master will release them, and they immediately turn on their tormentors. The elves never stand a chance.
During Iji's departure from Sector 3 during a Pacifist Run, she will mention the truce between her and the Tasen to Elite Krotera, who goes apeshit and screams about "worthless Vateilika" before announcing his intent to kill her - after Iji herself bites the big one. Krotera, you may Talk to Vateilika's MPFB now.
Vateilika: I've heard enough of that, thank you.
In Odin Sphere, the dragon Belial kills one of the Wise Men that had enslaved him with the last bit of energy he had left.
In Darksiders, Uriel refuses to save Abaddon from War while he begs for her help. Given everything he's done up to that point, Uriel telling him to "f*** off and die" despite her past feelings for him makes perfect sense.
Starting with Crash Bandicoot 3: Warped, Dr. Neo Cortex, the Big Bad of the first two games, ends up The Dragon for Uka Uka, an evil spirit inhabiting a tiki mask, and spends several games fearfully trying to keep the mask pacified. By Crash Mind Over Mutant, Cortex has teamed up with his old partner N. Brio and captured Uka Uka as the power source for the latest world domination plot.
Cortex:I used to run this show, and it's time I did so again!
In Dragon Age: Origins (specifically "The Stone Prisoner" DLC), part of Shale's backstory is that, after years of ill-treatment by Wilhelm, Shale ended up killing him. There is some ambiguity over possible outside influence however, and Shale claims not to be able to remember the incident. Whether it was intentional or not, Shale's vindicated satisfaction makes it this trope.
Then let's not forgot the great pigeon massacre that is unleashed by Shale after years of being pooped on by birds.
You can make these happen in Fire Emblem if you so desire, by having the right unit take out the right boss. The biggest example comes from Fire Emblem Awakening, if you let Say'ri kill Excellus.
In Paper Mario: The Thousand-Year Door, Vivian pulls a Heel-Face Turn because Mario was kind to her in helping her find something that Beldam dropped and forced her to look for as punishment. The next time you face the Shadow Sirens, she can be used as a partner.
Vivian: I'm with Mario all the way! Today, Sis, I am going to punish YOU, do you hear me?
In The Elder Scrolls V: Skyrim, the Dragonborn can choose to help the king of the Forsworn escape and take his revenge on the man who imprisoned him and used him to make the Forsworn kill for him under the guise of terrorism.
Another Skyrim example is Arondil, a necromancer who uses the undead spirits of young women as sex slaves. Stealing the soul gem from the pedestal behind Arondil's throne will result in two of his ghostly servants turning against him and murdering him.
This is essentially the plan for The Empire against the Thalmor; bide their time, pretending to be a Vichy France like state until the time is right to invoke this trope.
In the time skip between Oblivion and Skyrim, the Argonians, a race that's always discriminated against and were enslaved by the Dark Elves of Morrowind invaded and occupied the southern end of the country after the red mountain erupted, driving out the thousands of Dark Elves they didn't kill outright.
Imperial Agent: You get brainwashed so that you can't refuse a command by an SIS agent (and being that SIS thinks you're actually on their side, they order you to do things you probably don't like if you're faithful to the Empire). When an SIS agent is badly injured and cannot utter the keyword required to make you fulfill orders involuntarily, you have the option to let him bleed to death and remark spitefully about his condition, thus letting you indirectly bite him back. Later you can free yourself of the brainwashing and kill all of the SIS agents you were in contact with while being a double agent.
Subverted in Mass Effect with the geth. In the third game, after witnessing atrocities committed by the quarians during the Morning War, including attacking geth sympathisers, you have the opportunity to let the geth destroy the quarian fleet when the quarians attack them. However, the geth actually have no ill-will towards their creators, and later a geth prime shows genuine regret for being forced to destroy them.
A straight example with Khalisah al-Jilani, who has the opportunity to knock Shepard flat on his ass, in revenge for his decking her twice before.
In Metal Gear Acid 2, Vince was the leader of the security forces at SaintLogic, and attempted to quell the situation at the island and take care of the intruders (Snake and Venus). When he learns that his boss, Rodzinski, is planning to ditch the security forces to take the blame for the Praulia Massacre after the ICC reneigned on the deal, he orders his men to shoot his chopper down.
In Alpha Protocol, there is a sequence in the Grand Finale when you have a dual boss battle with Alan Parker and Conrad Marburg as part of a Timed Mission. However, depending on your actions previously in the game, you may have learned of something terrible that they did to each other, which you can then reveal to one to get him to turn on the other. If you discovered that Madison was Parker's daughter and Marburg killed her in Rome, you can tell Parker and he will attack Marburg, getting himself killed in the process and wounding Marburg just ahead of your fight with him. If, on the other hand, you got 100% of Marburg's dossier and 80% of Parker's before embarking on the mission, you can tell Marburg that Parker was the analyst who hung him out to dry, ruined his career, and nearly got him killed on his last mission for the government years ago. Marburg will knife Parker in the back, and you will face him alone.
Narrowly averted in Injustice: Gods Among Us, where after getting grounded for being useless against the Insurgency Lex Luthor Harley Quinn tries to kill Joker. It was thank to Luthor's timely intervention that she put the knife down.
In Skies of Arcadia, Galcian would have survived having his doom-base destroyed by the heroes and being beaten up in personal combat if he hadn't backstabbed and tried to kill Belleza. Belleza answers his betrayal by ramming his escape pod and killing them both.