In 7 Seeds, Gengoro sees it as his duty to kill all the animals he had previously taken care of in Animal Class, after they had been let loose in nature where they are confused, perhaps with stunted survival instincts or were flat out infected with rabies. Especially hard was Gengoro killing the tiger Tango, whom he had practically raised.
In Aldnoah.Zero, a flashback reveals Lt. Marito shot and killed his friend and fellow soldier Humeray at his request, as he was trapped in his tank and was burning alive. This is explained to be the cause of Marito's PTSD, as well as Captain Magbaredge's initially hostility towards the Lieutenant. (Magbaredge is revealed to be Humeray's younger sister.)
In the anime series spinoff of Arc the Lad, the hero Elk encounters his long lost childhood friend, changed into a barely sentient womb for the terrible monsters the bad guys are using as mooks. He strangles her to end her suffering.
In the end of Assassination Classroom, Korosensei's death felt more like an unnecessary execution than an official assassination, no one from Class 3-E is happy about this and Nagisa is the one who holds the horrible burden to kill Korosensei. They had no other choice otherwise the government will bombard the mountain to take the credit.
Attack on Titan deals with this on several occasions, primarily with people considering the option when faced with being devoured by Titans.
The ritualized inheritance of the Titan powers combines this with elements of a Human Sacrifice. When a previous holder begins dying from the Curse of Ymir, a successor is chosen to kill them and inherit their powers. A flashback shows that by the time Uri Reiss passed on his powers to his niece, he had begun to waste away from the Curse.
When they are reunited after the 4-year Time Skip, Reiner begs Eren to kill him rather than continue living with the trauma and guilt of his actions. Eren refuses to do so, expressing sympathy for his former comrade.
Eren and Reiner are in a fight against each other after the time skip and Reiner tries to kill Eren as his faction plans to do. He knows he and the others and Eren especially have suffered unimaginable torment and trauma and he wishes to end the suffering, and Eren's especially. He figures as they are Titans, he and Eren are going to die in a few years with their limited lifespans, anyways. He also feels he will kill two birds with one stone: he will prevent Eren from ending humanity and he will end Eren's immense trauma from all he went through by killing him.
At the end of Black Butler's Circus of Fear arc, Ciel orders the destruction of the villain's lair, including all the surviving children whose minds have been broken. Though it could be less to do with sympathy or kindness and more to do with Ciel wanting to remove everything that reminds him of his traumatic past.
Black Jack's rival, Dr. Kiriko, is a physician whose medical practice consists entirely of euthanasia. This is due to his nihilistic outlook, developed as a military doctor, which stipulates that resisting death is an exercise in futility.
Killy destroying the eternal cloning machine and it's sole occupant in Blame! could be viewed as a mercy kill.
In Canaan, Alphard has Liang Qi killed after she goes into a full mental breakdown that concludes with her trying to give herself synesthesia and suffering a Super-Power Meltdown... sort of.
Towards the end of Chrono Crusade, Fiore offers to do this for Satella after she's badly wounded in a battle with each other (the alternative being to leave her to be killed by the feral demons they're surrounded by). Satella Takes a Third Option and uses her "jewel witch" powers to freeze them both in crystal.
C.C. does this to Mao in an earlier episode after Mao had just been rendered unable to ever speak again, using the closest thing to an Instant Death Bullet ever seen in the series.
Akito the Exiled has this as Jean's reason for killing Shin in the finale, at the cost of her own life. After taking a lethal impalement from her commander to save Akito, then shooting him point-blank, Jean declares to Shin that she no longer wants to see the man she loves suffer emotionally and mentally, having seen a tormented man who hates the world for all it is. Thanks to her, Shin's wrath disappears and he dies peacefully alongside her.
Day Break Illusion: This is basically the role of Elemental Tarot users. The magical girls have no way to purify the Daemonia-possessed humans, so they have no choice but to kill the human to destroy the Daemonia. Protagonist Akari's first kill was her own cousin Fuyuna, who was unknowingly infected by a Daemonia.
This is one way to view Light's death in Death Note. Only in the anime, though; in the manga, it's made clear that Ryuk has gotten bored.
Tanjiro's fighting style in Demon Slayer: Kimetsu no Yaiba has a special strike that is all about this. Form 5, "Blessed Rain after the drought". Tanjiro uses it against the Spider Demon Mother, who experiences it like a gentle rainfall.
Delicious in Dungeon: Laios ends up having to strangle his sister to death after she's been turned into a mind-controlled draconic chimera by the Mad Sorcerer. It clearly pains him to do so and his party members are incredibly disturbed by the sight of it, but they know it's a necessary action if they want to turn her back to normal and defeat the Sorcerer.
In the last episode of From the New World, Saki does this to Squeala/Yakomaru after he's sentenced to a Fate Worse than Death and she realizes he is technically human.
Noble Demon Scar does this to Nina Tucker, whose father had transmuted both her and her dog Alexander into a pitiful chimera. His comments beforehand make it clear he does this not out of disgust for Nina herself, but rather because he pitied her and thought that death was a kindness for her.
In order to escape from Gluttony's stomach, Ed has to use some of the souls attached onto Envy in order to open the gate. One of them even thanks Ed for being put out of his misery.
This is truth behind Takiko Okuda aka Genbu no Miko's death in the original Fushigi Yuugi: Miaka's brother Keisuke and his best friend Tetsuya found out that Mr. Okuda killed her to stop her being devoured by Genbu and then killed himself. Fushigi Yuugi: Genbu Kaiden shows how it happened towards the end - Takiko was already dying from tuberculosis as well as being devoured after summoning Genbu, so Mr Okuda bonds their lives together note (he was holding the Universe of the Four Gods magic book in his hands, and Takiko was inside the world of the book) and commits suicide to ease her suffering. Takiko explains this to her Senshi as she lays dying and has no bitterness towards her father, as she says he wanted to help her.
Averted in Fushigi Yuugi: Byakko Ibun, where Reipin begs her Only Friend Nirusha to kill her and use her bones in his protective charms after she both reveals herself to be a Shapeshifter and destroys her village. Nirusha refuses and tells her that she's a human, and she returns to her human form in tears.
In Garei Zero, Kagura kills her surrogate sister Yomi after the latter is possessed by a cursed stone.
A variation in Gintama where Hijikata grants one to the dying and disgraced Ito who had betrayed the Shinsengumi in the form of a duel so that the latter could die honorably instead of dying alone as a traitor from bullet wounds.
In Goblin Slayer, the Rookie Mage is stabbed in the stomach by a goblin knife, one infected with a poison. By the time Goblin Slayer finds her, it's too late for an antidote to be given, and she is in excruciating pain, so she asks the Goblin Slayer to kill her. He obliges with a small blade to her neck. All of this takes place in the first episode, to let the viewer know what they're in for.
Mobile Suit Gundam 0083: Stardust Memory: A Zeon soldier, disgusted at the sight of a Zaku painted white and used by the Federation, resolves to give it a "mercy killing".
In Mobile Suit Gundam Wing: Endless Waltz, Heero offers this to the critically injured Mariemaia after the final battle. When he pulls the trigger, it is revealed that he is out of ammo.
In Hellsing, when a human is turned into a ghoul, there is no turning them back, so the Hellsing organization agrees that it's best to take them out quickly as a mercy kill.
It's also the real motivation of why they kill monsters that threaten their country. Aside of their duty to keep it safe.
At least twice in Highschool of the Dead. The first time, Hisashi isn't killed until after he turns (despite asking to be killed so he wouldn't, and Takashi considers this as his personal Moral Event Horizon crossing), but the second time goes over without a hitch.
Subverted in Hunter × Hunter's first anime adaptation. Killua wants to mercy kill a bear cub that was mortally injured by a sniper, thinking that there's nothing they can do to for the baby, but when he's going straight for the kill Gon's aunt Mito extends her hand and blocks the lethal blow. She then convinces Killua to not do it, saying the cub hasn't given up on life, and Gon convinces Killua to heal the cub through Nen. They do; the baby is soon saved and returns to his family.
When he was sent to Earth, Jaco the Galactic Patrolman had specific orders to use an Extinction Bomb, an artificial plague that would wipe out every form of life on the planet, if it turned out the alien he was sent to kill was an adult and thus too strong for him, as mankind would have been annihilated anyway but the effects of the Extinction Bomb would have been much quicker and less terrible. The moment he identifies the alien as a Saiyan from Planet Vegeta, the reader understands that his orders were fully justified.
In K, Reisi is forced to do this to Mikoto to prevent the latter's Sword of Damocles from falling and kill thousands of innocent people.
In King of Thorn, Ron decides to mercy kill the child Tim, believing there is no hope of rescue and that a quick death by bullet is better than being eaten by monsters or petrified by Medusa. Katherine isn't ready to give up hope, however, and just barely manages to prevent him from shooting the boy. Tim, asleep, doesn't even realize what almost happened.
In Kinnikuman Nisei this is what causes Ashuraman to make a Face–Heel Turn after he murders his son when he learned of his past as a Devil Chojin and killed his mother in a fit of insanity.
In Juni Taisen: Zodiac War, this happens more than once and always in relation to Rabbit's powers. Ox performs a mercy kill at the request of Tiger, to prevent her from becoming one of Rabbit's zombie minions, and is later himself killed by Rat to escape the same fate. A flashback later reveals that Monkey requested that Rat do this, if she were going to be killed by Rabbit. The information she gave him allows him to finish off the zombies of Rabbit and Monkey once and for all.
In Muv-Luv Alternative: Total Eclipse, Kazusa is trapped and being swarmed by BETA, and begs to be killed by gunshot before she can be Eaten Alive. The trope is averted. Yui empties her gun trying to comply, only to miss every single shot. Kazusa remains visibly alive, jostled as her body is eaten free of the wreckage. She doesn't die until they finally tear her disemboweled upper half out of it.
In One Piece, Pica's response to having his helium voice laughed at is to bury the offender alive. Due to this, one of Doflamingo's other enforcers will typically just shoot you dead before Pica can get to you, as your family will at least be able to bury you properly that way.
Certainly Tsunayoshi viewed her death at the hands of Yoshiyasu as this in Ōoku: The Inner Chambers: she had long believed that she became The Wrongful Heir to the Throne and would welcome someone to kill her. It's unclear though if Yoshiyasu killed her to fulfill this trope or if another trope motivated her murder.
Kyouko sacrifices herself to kill Sayaka after Sayaka turns into a witch.
In one of the attempts for Homura to Set Right What Once Went Wrong, she's forced to shoot Madoka before she can turn into a witch at Madoka's own request. Earlier that same timeline, Mami does this to Kyouko after realizing what's going to happento them. She was going to do this to Madoka, Homura, and herself. The only reason she doesn't succeed is that Madoka does it to her first.
In a way, dying from battling a witch and getting your soul gem destroyed seems like a fate much kinder than turning into one. In fact, this is what the witches are trying to do by killing humans — sparing them from a life of slavery to the Incubators.
Madoka does this in a world wide scale in the Grand Finale. Her wish says that she wants witches to not exist anymore, so she spreads her power all over the world helping magical girls in need. In the case of magical girls whose Soul Gems are completely corrupted so they're about to become Witches, she can't save their lives, but at least she can make sure they'll die painlessly and peacefully while their energy is collected to save the world. (This includes Sayaka, who can pass on in peace now.) And in a sense, she also does this to herself: since she's destined to become the most powerful witch right after becoming a magical girl, Madoka ends up erasing herself outta existence when done, after a last talk with Homura.
Attempted in Rosario + Vampire, where Tsukune became a ghoul. Thankfully, Moka was stopped before she could land the finisher.
This almost occurred in School-Live! when Kurumi was bit by a zombified Megu-nee. Her friend Rii was panicking over the prospect of having to kill her however Miki came just in time with the Magic Antidote.
In Speed Grapher, Suitengu did this to his little sister, Yui, after discovering that years of abuse and degradation in a brothel had destroyed her mind.
Street Fighter II: The Manga has this happen with Charlie, who was one of Bison's first test subjects and went insane from the Doll drug. Guile intercepted him as Charlie was attacking unarmed villagers, and was forced to kill his best friend to prevent more lives from being endangered.
In Vinland Saga Askeladd tries as such for his fatally wounded friend Bjorn but he screws up the blow, missing the man's vitals. He rectifies this mistake shortly after a few last words between himself and Bjorn.
After another failed assault on London, a viking is walking through the camp with the wounded, asking if anyone needs a finishing blow to both die less painfully and, according to their beliefs, go to Warrior Heaven. One warrior in the picture is even calling over to him to take up his kind offer. In particular they go around to see if anyone is suffering from an Agonizing Stomach Wound, which was a certain killer, and putting those guys out of their misery.
Askeladd himself offers to let Thorfinn Mercy Kill him after he's stabbed fatally by Canute, more for Thorfinn's benefit than his own since he knows he's bleeding out anyway. Thorfinn is too messed up to do it.
In the final episode of Wolf's Rain, Hige is mortally wounded by Darcia. When Tsume arrives and finds him slowly dying, Hige convinces Tsume to put him out of his misery. The grey wolf reluctantly does so by crushing his neck.
In YuYu Hakusho, Yusuke is fighting Team Ichigaki, made up of three fighters who have been enslaved by a sort of brain parasite; they mindlessly attack, saying only, "Kill...kill...kill." At one point, they manage to regain just enough control to finish the sentence: "Kill us." Yusuke resigns himself to the fact that they'll never be able to break free on their own, and he can't do anything for them except, well, this trope. Fortunately, the Masked Fighter intervenes with a technique which frees them.
