Subverted, averted and inverted in the span of only a few seconds in Death Note. After Light is revealed to be just a human with a note and a bunch of bullets in his chest, Mikami Goes Mad From The Revelation, but instead of turning on him, (some say) stabs his arm with a pen (and kills himself in the process) to allow Light to run. Also Light takes good care to subvert this as much as possible with his other "doggies": he "writes in stone" everything Takada will do, leaving no chance for her to retaliate in any way and positively reinforces Misa to do anything he wants (otherwise he'd just kill her as fast as he could) and ultimately makes sure she won't bother him in his part of his life as Kira by forcing her to renounce her Note.
It's also played straight when Matsuda shoots Light after an entire series of trying ti help but not being able to, after Light says he was manipulating Matsuda's trust the entire time. Light himself is shocked by that, having figured that Matsuda would be the one most loyal to him...
Subverted in Monster. Johann didn't need help to be a monster and he didn't care enough about his creators to take revenge. He kills them anyway.
Siri eventually gets to give Bride, a man who forced her into a cult "marriage" and tortured her constantly for several months, his comeuppance by holding him over the edge of a cruise liner by his arms as its sister ship slams up against it. Severed limbs ensue.
In Fullmetal Alchemist, Solf J. Kimblee gets his throat torn out by his ex-bodyguard Heinkel, who Kimblee almost killed twice during his battle with Ed and another with his brother Al.
Kimblee himself does this to Pride, who had absorbed his soul following his "death".
Dr. Marcoh also stuck it to Envy by laying out a trap with his travel partners, after Marcoh had been held captive with his home village as hostage. Envy went from One-Winged Angel to Clipped Wing Angel once Marcoh was done with him.
In the end of the 2003 anime version, Dante was killed by Gluttony after she erased his memory to turn him into a mindless monster.
In Crows, Hideomi Kunou gets Yamazaki to sell out his friend Bandou, who gets his ass kicked before getting run over by a motorcycle. When everything falls apart for Kunou, Yamazaki returns to pay him back in kind.
Subverted in Toward the Terra. Keith Anyan is repeatedly abusive towards his subordinate Jonah Matsuka and informs him that once the war against the Mu is over, he'll be disposed of; he asks if Matsuka will kill him before that happens, apparently deliberately trying to needle Matsuka into doing just that. Instead, Matsuka sacrifices his own life to save Keith's - to Keith's considerable surprise and dismay.
In Pokémon Special, Blue really didn't appreciate being kidnapped and being forced to become someone's underling, so she swiped the Applied Phlebotinum on her way out escaping, setting back the Big Bad's (named the Mask of Ice) evil plot for several years, and actively looked for ways to take him down. Granted, she didn't deliver the finishing blow, but she was a big part of it nevertheless.
The anime likes doing this with the Fire type starters under Ash's care — Charmander and Pignite blasted their abusive former trainers with Flamethrower, while Chimchar evolved all the way to Infernape after being released by Paul and was the lone Pokemon left on Ash's side at the end of the Sinnoh League battle.
Shadow: I came out of the Dark Mirror, and with its power woke you. How fitting that I use it to destroy us both!
In Digimon Adventure, Myotismon raised Gatomon as a minion but abused her on a regular basis. While she has some loyalty to him, it's ultimately destroyed when she discovered she had a choice in the matter and to be good; maybe if he'd treated her better recent events wouldn't have happened. Then he goes and kicks one dog too many and kills her best friend Wizardmon, resulting in Gatomon digivolving and killing Myotismon.
Wizardmon himself might count too as by the time he attacks Myotismon (from behind) drawing first blood it should added. Myotismon has abused his best friend as mentioned above, tried to drown him and presumably subjected him to the same abuse as all the other people who work for him.
Happens AGAIN with Myotismon at the end of Season 2. He possessed Oikawa to put Dark Spores inside some kids who think their dreams have been taken away, harvesting them to come back to life as MaloMyotismon. When the darkness is getting stronger and it seems MaloMyotismon has won, Davis says he wants to open a noodle cart and work hard on it, which causes the kids to speak of and regain their dreams, destroying Myotismon's body and setting the stage for his spirit form to be destroyed soon after.
In Sakura Gari, this is Tomohiko Katsuragi's perdition. The three persons whom he abused the most ( Masataka, Souma, and his own wife Asayo) are the ones who orchestrate the spectacularHumiliation Conga that he suffers and which finishes in a fiery Karmic Death.
Sakon Daimaru from Gamaran had his life and mental sanity ruined by his elder brother Ryuugo, who even yelled at him for losing his battle against Gama. This prompts Sakon to go insane and snap Ryuugo's spine as soon as he turns around.
In Soul Eater, Chrona stabs their mother, Medusa to death after all the nightmare-inducing experiments she ran on them.Although that's a bit misleading. They don't kill her because of how horrible she is, they did it because Medusa was suddenly acting like a real mother, such as cooking their favorite meal for them and apologizing for all the things she did, even hugging them. But Chrona is so insane from the experiments and so shocked by this that they assume that this is an impostor. And in the end? The last thing Medusa says in the chapter confirms that this was all part of her plan...
In Jack to Mame no Ki, throughout the movie the witch Hecuba insulted and abused her son, the giant Tulip. Eventually he had enough; when she told him to finish Jack and Margaret, he chose to kill her instead, by stepping on her.
In the final episodes of Kirby of the Stars (Brought to the US as a DVD movie Fright To the Finish), when Dedede meets the Holy Nightmare salesguy, the first thing he does (Besides comment on Salesguy's height) is force-feed him a spoonful of Kawasaki's awful cooking.
Salesguy:(Washing his mouth out) That was completely disgusting!
In the Commander Red Saga, Black, after narrowly surviving being knocked out of a window and being flattened (It Makes Sense in Context), overheard Commander Red's plan of wishing to Shenron to become taller. Black then confronts him on this, having earlier been led to believe, alongside the rest of the Red Ribbon Army, that the wish was meant to be for World Domination. After Red not only protests Black's accusations, but also Kicks The Dog one time too many by implying that the reason why Black's upset is that he's jealous that he isn't commander, and that he deliberately made Black an expendable lackey while also claiming that Black is pathetic even for that, Black decided that was the final straw and proceeded to execute him by shooting him in the head.
In Movie 8 of Dragon Ball Z, Broly, the titular bad guy, finds his dad Paragus (who is pretty much the true main antagonist throughout the film, even with Broly being the central main antagonist), planning to abandon him to the soon-to-be-destroyed planet in an escape pod which, as Broly noted, was only built for one person, to which Broly promptly returned the favor by crushing the space pod that Paragus was inside and then throwing it like a discus to the comet. The fact that Paragus had earlier fitted him with a Hypno Trinket and presumably used his powers to destroy the galaxy against his will earlier in the film was probably a large contributing factor to Broly's decision to kill Paragus as well.
Similarly, Majin Buu gets tired of Babidi's verbal abuse and threats to seal him up. The result is predictable.
In The Big O, a kitten who became attached to the robot Dorothy is abducted and experimented on by a Mad Scientist after killing its original owners. Said kitten monster trashes Roger and his robot companion a bit before Dorothy helps it come to its senses, whereby it grabs the scientist goading it to kill Dorothy with its giant tentacle and snap his back offscreen.
Buhpu, having killed Ivy Cortlaw to manipulate her brother Kid into fighting the MLS by making him think they had killed her, gets killed by the one he had manipulated when the truth comes to light.
In a similar case, Teeki killed Enchu's mother, with the ultimate goal of taking Enchu's body, and Muhyo revealing the truth behind this results in Enchu resisting Teeki's possession and enabling Muhyo and Roji to finish Teeki off
The ending of Puella Magi Madoka Magica can be seen as this. Kyubey doesn't directly hurt Madoka, but he sure doesn't hesitate to inflict horrible tragedy on her friends, with the intent of forcing her to make a contract no matter how much her life gets screwed up in the process. His over-the-top heartless abuse convinces Madoka, who had openly refused to given in for the entire series, to invoke Laser-Guided Karma on him and his entire species, and the entire universe via contracting and then turning her wish into something that totally screws with the Magical Girl System led by Kyuubey, sacrificing herself in the process and then ascending to pretty much god-hood.
Shown again in Rebellion.Kyubey's machinations end up causing Homura to gain godlike powers like Madoka... except she becomes the Devil to Madoka's God. And she has absolutely NO problem making Kyubey's life and that of his entire race a merry Hell. Everyone else is spared though.So to speak.
In Claymore, when Cassandra the Dust Eater was alive, she was massively screwed over by Roxanne of Love and Hate. Not only did Roxanne leave Cassandra's only friend amongst the Claymores to die at the hands of a youma, she also bashed Cassandra herself over the head when she tried to fight her way through a horde of Claymores to get her revenge, causing her to be cut down and killed. Fast forward some years later, and the two of them - along with Hysteria the Elegant - are resurrected by the Organisation and eventually awaken. After Roxanne uses up all her weapons fighting Miria and is rendered powerless, Cassandra happily chows down on her, giving her a well-deserved Karmic Death.
In the Luxury Liner case, Ichiro Hatamoto kills his grandfather Gozo after he is being fed up by the abuse when Gozo cruelly mocked him andrefuses to let him marry Natsue, the girl he loved, who also happens to be Gozo's granddaughter.
In a filer case, the Kimono Goddess legend tells that Ohana's angry spirit kills the two greedy local girls who caused her unfair death. Even more symbolically, their lifeless bodies are found surrounded by the kimonos that the two girls wanted enough to get the real owner of the kimonos killed.
In One Piece, the villain of the CP 9 saga, Spandam has spent the entire arc beating Nico Robin mercilessly without any way for her to defend herself, as well as saying anything he can to break her spirit. Once she ends up breaking free, she pins him down, smacks him in the face over and over, then finishes it off by snapping his spine nearly in two. This doesn't kill him, but it ends up making him suffer a Fate Worse than Death due to him being crippled for life while the group of assassins he was the former boss of is out for his blood.