This is how fights usually turn out in One Piece. Luffy attacks with intent to kill, but if an enemy's already defeated, he'll decide said enemy should instead live with all his hopes and dreams shattered. Occasionally however, some villains actually end up recovering from their loss (Wapol for example became an incredibly wealthy toymaker and tyrant of another kingdom and Eneru went to the moon like he originally wanted).
In Dragon Ball Z, Goku planned to do this with Frieza when the latter ceased to pose a threat to him near the end of their battle on Namek. "Live with the shock. Keep it bottled up inside you, silently." Later, after Frieza lost his limbs, Goku told him to drift about in space and contemplate his defeat. It didn't work either time: the reason he lost his limbs is because he got hit with his own energy disc, and when Goku gives him some energy to at least survive, he turns right back around and tries to kill Goku with it, earning him a blast to the face. And then he comes back as a cyborg, still itching for revenge.
Happens to Ritsuko in episode 23 of Neon Genesis Evangelion. After revealing the secrets of the Terminal Dogma and of Rei and the Dummy Plug System to Shinji and Misato, Ritsuko realises that Gendo used her, and destroys Rei's clones. She then breaks down into tears, inviting Misato to shoot her, saying that she welcomes death. Misato refuses, saying that Ritsuko is a fool for saying so.
In Fullmetal Alchemist, Scar does one of these toward Dr. Marcoh and really makes it clear that post-Heel-Face Turn, he's still an Anti-Hero. Marcoh comes to Scar admitting that he had created the Philosopher's Stones which were used to wipe out most of the population of Ishval (Scar's country). While Scar has in the past killed state alchemists for less, he's cooled by this point and is also taken aback when Marcoh begs for death (Marcoh had been threatened by Lust and Envy that if he didn't make another Stone for them, they would kill Macoh's entire village). So, what does Scar do? He "helps" Marcoh to fake his death by using his powers to horribly disfigure his face.
And by this point, Marcoh loathes himself so much that he doesn't really care. While he has the skill and opportunity to repair the damage later, he decides to keep it as penance.
It as well served a practical purpose: No one besides the homunculi were able to recognize the disfigured doctor, allowing him and Scar's group to travel with more ease.
In Samurai Champloo, a previous comrade of Mugen betrays him so that she will not be alone; something she's terrified of. He kills everyone in the old crew who betrayed him and then just ignores her; even when she asks him to kill her so she can be Together in Death.
Hiei of YuYu Hakusho was ordered killed by the village of his birth due to the expectation that any male child born to their One-Gender Race of normally Truly Single Parents would inevitably destroy them if allowed to grow up. Years later he returned to do just that, but, after seeing the pitiful lives the villagers lived, he came to the conclusion that killing them would only end their misery.
In Noir, after Chloe reveals that Kirika was the one who killed Mireille's parents, Kirika begs Mireille to keep the promise that she made in the first episode and kill her. Instead, Mireille walks away, severing their partnership and leaving Kirika with the knowledge that she is now alone. They reconcile in the penultimate episode.
In Fist of the North Star, Kenshiro ends up doing this to Souther, partially. While he does ensure that Souther eventually dies soon enough, the fact that he actually does show mercy to Souther is the dagger through the heart of Souther, who himself had sworn off all kinds of mercy, making it a heavy blow onto his pride. Possibly Amiba as well. Kenshiro doesn't directly kill him and mocks Amiba's inability to avert his fate.
Ginga Densetsu Weed: Hiro leaving Kamakiri to recover by himself (not likely) comes to this. Hiro has left the Irish Wolfhound wounded, bloodied, de-fanged, and castrated on the ground, but instead of killing him for killing his father when he was a puppy, he leaves him there after saying to live with his wounds to understand the feelings and pain of others. Kamakiri tries to attack him one last time...but fails, leaving him howling in pain and rage as his death arrives.
The ending of Revolutionary Girl Utena can be seen this way. Rather than actually killing or hurting Akio, Anthy simply walks out on him, leaving him powerless. Since there wasn't really too many ways to kill him anyway, it mightn't have been mercy, as such. But this is Utena. If she wanted to, Anthy would have found a way.
The ending of Senki Zesshou Symphogear G has Genjurou sparing Dr. Ver, preventing him from attempting to kill himselfupon witnessing all his plans unravel when Maria, Kirika and Shirabe, Symphogears he manipulated to advance his goals of making himself look like a hero by exploiting the chaos of the moon crashing into the Earth courtesy of Nephilim, his creation, finally wised up and joined Hibiki, Tsubasa and Chris to stop Nephilim. Genjurou's reasoning is that he's not going to let Ver be written off as having pulled off a "Heroic Sacrifice" in the attempt to stop the moon's fall, instead making sure he's going to see justice done. It was so bad by the end he's reduced into a giggling fit as he was being led away on handcuffs.
Batman has done this a few times, as his policy can make it a necessity; in one instance, a man inadvertently killed a mutual friend as part of a revenge spree, but destroyed the evidence. Batman forced the killer to stay in the same small town, referring to it as the killer's "prison," and returned once a year to make the guy sit at the gravesite of the friend he rued killing.
Similarly, in Kingdom Come, the evil members of the Mankind Liberation Front are ultimately forced into helping care for the survivors of an attack they helped launch; Lex Luthor is especially galled at having to empty bedpans.
Or the time he tracked down the black ops agent who helped frame him (Bruce Wayne) for murder. Since there was no evidence of the man's existence, he couldn't be tried, so Batman put him in Arkham. The spy tells the doctors that he's not crazy; he's a secret agent who framed Bruce Wayne for murder and there's no record of the mission because he was tasked directly to the president. None of the doctors believe him.
Batman: You came close, Joker. Just minutes from death.
Joker: But I'm still HERE bay-bay!
Batman: That's right. And when you're sitting here alone... in the middle of the night... unsleeping in the dark. Remember... every breath you take you owe to me. What's the matter? Don't you have any jokes for me?
Captain America does this inadvertently sometimes. His enemy Flag-Smasher once went into a lengthy Motive Rant about how he couldn't stand knowing Cap was simply a better person.
In the comics, Bullseye's hatred of Daredevil was actually exacerbated after the hero saved him from an oncoming subway train, which Bullseye considered a humiliation. He gets a nice little speech about it in the issue where he breaks jail and kills Elektra.
Jesse Custer of Preacher gives up killing with his Word powers about a third of the way through the series, but his alternative punishments for enemies generally turn out even worse for them.
Similar to Cap, Superman seems to do this to Lex Luthor on an almost daily basis without even trying. Apparently, Lexi's ego is so enormous that having a man more powerful than him, who uses his might out of genuine altruism and refuses to work for him is so incomprehensible that it galls him like nothing else ever could.
In one Spider-Man story in the early 2000's, a particularly ugly fight between Spidey and the Green Goblin (the Goblin had just crippled Flash Thompson) ended with Spidey coming within a hair's breadth of finishing Norman off. Spidey spares him, and later tells him that just being a person as horrible as Norman is its own punishment. Norman's reaction implies he sees the truth of this.
Ghost Rider actually has this trope as one of his powers. His Penance Stare does no physical damage, but forces his opponent to feel every single bit of pain or evil they infliced on others. Most recover, but have something to think about for the rest of their lives.
This is what Cyclops decides to do to Kaga, the crippledevil geniusBig Bad of Astonishing X-Men #31-35, who hates the X-Men because they're a bunch of incredibly attractive people with superpowers, whereas he is a realistic mutant, sickly and deformed as a result of being born to a Hiroshima survivor. After Kaga's Motive Rant, Cyclops decides to arrange for Mutants Sans Frontièresnote Warren Worthington's X-Men-affiliated charity organization medical funding to be used to take the best possible care of him until he dies of natural causes.
In New X-Men, Emma Frost, upon catching Kimura trying to assassinate X-23, proceeds to explain to the nigh-invulnerable villain exactly why she acts the way she does by pointing out that she only does what she does to X-23 because of her childhood before erasing her one and only happy memory and then sending her off with the psychically implanted suggestion of hunting down her employers.
In the 2010 Wolverine- Mr. X one-shot, thetitularvillain, having lost once before to the titular hero, trains obsessively for months to prepare himself to counter Wolverine's berserker rage, then lures Wolverine into a fight. But Wolverine refuses to let him trigger his rage and ultimately refuses to fight him at all, realizing that leaving Mr. X forever wondering Who Would Win will cause him more torment than simply defeating him.
A particularly nasty example is Wolverine's treatment of Matsu'o Tsurayaba, the Yakuza boss who killed Wolverine's lover Mariko. Every year on the anniversary of her death, Wolverine fought his way past Tsurayaba's defences, took a piece of his body, and left him alive. This was taken to the point of Wolverine actively stopping Tsurayaba from killing himself or anyone else from killing him, because Wolvie wanted him to suffer as long as he did. By the time we find out about this, Tsurayaba is missing a hand, an arm, a leg, half his face, and his body is covered with scars and medical implants.
In American Vampire, infamous outlaw-turned-vampire Skinner Sweet attends the book signing of a writer who was there back when Sweet was turned, and has since made a fortune from his one novel, a fictionalized account of the outlaw's story. Sweet exits the event, leaving behind a note saying "You are old and I am young for eternity. So I let you live to suffer and die. Why not? What better revenge is there than that?"
In a flashback in Planetary#7, JackCarter happens to run into an Invisible man, who explains that he's "this year's Herod", a Punch Clock Villain sent by the government to kill a pregnant local prostitute just in case she's carrying the second coming. Disgusted, Carter does a seemingly ineffectual spell and walks away. When the Herod goes to continue his mission, he finds he's been trapped on that street corner in an invisible forcefield only a few feet in diameter. For the rest of his life.
Played with at the end of the Young Justice comic book; when Secret turns back to the light side,Darkseid takes "revenge" by restoring her to life as an ordinary mortal. Though he considers this cruel mercy, in reality it's exactly what she wanted.
Towards the end of Nikolai Dante, Arkady/Dmitri has both Jena and Nikolai kidnapped, and says he'll stop torturing Nikolai to death if Jena marries him.
The first time Morpheus goes to Hell, he escapes by pointing out that "What terrors would Hell hold if those entombed within could not dream of Heaven?" This gets kicked up a notch when Hell is taken over by a pair of angels after Lucifer abandons his position. The two decide that horrible things will still happen, but for the purpose of reform instead of punishment. This makes everything so much worse, because it implies a false hope that the torment of the damned might someday end. Key word being "false."
New Republic commander Mirith Sinn is captured and tortured to learn the location of an enemy of the Empire. She holds out until the Big Bad orders an orbital bombardment on her men's secret fallback position. She dejectedly gives him the information he wants...and he orders that the bombardment continue until every last rebel is dead. But he keeps one part of his deal...he lets her go.
During the events of "Dead End Kids", the Runaways become stuck in New York City in 1907, where they encounter past versions of Gertrude Yorkes' parents. When the Yorkes discover that their daughter is dead, they launch a plan to nuke the city to kill the Runaways. It fails, and the Runaways' leader, Nico Minoru, decides to punish them by casting a spell that forces them to go back and live out the rest of their lives knowing that they and Gertrude will all die, and they can't do or say anything to stop it.
Nico: They'll go back where they came from. And they'll know. What happens to Gert, what happens to them, they'll know every second it's coming. They won't be able to change anything they do. Or say anything. Not even to each other. For all the world, their short, useless lives will play out exactly like they did before. But inside... they'll never stop screaming.
In The Noble Nine: A Kill BillEsque Tale of Revenge, Crono's only goal in life is to die a noble death in battle...so Samus, playing the role of the Bride in this story, spares him. The other seven members of the Nine are all dead by the end of the story—all by Samus's hand except for Sonic, who denies her the satisfaction of the kill by committing suicide in front of her.
In the fanfic The Girl Who Lived, Rose Potter takes the Harry Potter example mentioned further down and ramps up the 'cruel' factor by about a thousand percent. Harry persuades Sirius and Lupin to spare Pettigrew because he doesn't think James would want them to become murderers (and to help prove Sirius's innocence). Rose, OTOH, describes in rather ghoulish detail how much worse than death life in Azkaban will be for him, and this isn't even the creepiest thing she does.
In the Deep Space Nine Fanfic, The First Tile, a bereaved Trill father whose daughter's death was ordered by the planetary government hopes the monarch has a long life in prison.
"I'm glad he will spend the rest of his life in a prison, eating meager food, surrounded by cold walls, performing the same kind of labor many Unjoined spend their entire working lives doing. I don't want him to get out. I want him to spend the rest of his life remembering what he did to our world, and when he dies, I hope that even the wind forsakes him. I say that as a father, in the name of every other parent who will, or * has* faced the same truth."
In Frigid Winds And Burning Hearts, Princess Luna realizes that killing Captain Braveheart will just confirm in everyone else's eyes that she's a monster. So instead, she spares his life, and teleports him to his commander, telling him to have fun explaining his actions to his superior. Braveheart is not too happy upon hearing her plans. Unfortunately, this backfires, as he just tracks them down again and ambushes Twilight.
Mr. Evil'sOriginal Character Fredi Heat sees this method as worse than just killing them. Despite having no qualms about brutally killing someone that looks at him wrong (did I mention he is a "good guy"), he always sees it more cruel to take someone in alive rather than dead. As he quotes "'Alive' just means you can still breath on your own".
The courts decided not to prosecute John Patterson for letting his wife Elly go insane and then attacking her in The New Retcons because his reputation was already shot and it'd just be a waste of the court's time. John, having a Self-Serving Memory, thinks he beat the system however. He does eventually see their point when Christmas rolls around and he's all alone.
A Brief History of Equestria: After Hurricane's coup against Commander Sullamander, the latter's remaining loyalists tried to stage a counter-revolt and were effortlessly crushed. When Hurricane realized that his own (unloving and unloved) mother Star Saber was the leader of the revolt, he spared her — not out of familial obligation, but because he wanted her to live with her utter failure.
After Yue/Tui destroys Yuan's fleet, she lets him live to wallow in his failure and insignificance. Unfortunately for him, Shiyan is much less merciful.
And at the end of the story, Jiazin's first act as Fire Lord is to force Qing Xi into retirement as punishment for collaborating with the majority of Azula's crimes.
Grey Hoof suffers this in the Waking Nightmares chapter "A Blank Story, part 2". (Story Of The Blanks is considered canon.) After he's shown to have learned nothing from his punishment by transferring the curse to everypony in Ponyville just to save himself, Celestia decides he needs a more severe punishment... trapping him in the ruins of Sunnytown, alone, under a spell that makes him imperceptible to others (and causes them to avoid the area). The spell also keeps his mind calm and sane, as falling into madness would be a merciful escape, and Celestia won't allow even that.
In The Prayer Warriors, during The Evil Gods, Part 2, after Jason kills the Roman godSocrates, Thalia comes to him with one of Socrates' captured followers. The follower begs Jason to kill her, but he tells her he will not, because murder is a sin, and says she will become his slave and has Thalia take her away to be punished. This may also apply to a Communist Mook in Threat of Satanic Commonism, whom Jerry spares after cutting off his arms and legs and blinding him, so that he can suffer from his wounds and have the possibility of converting and going to Heaven.
The Bride does this to Elle Driver at the end of their fight in Kill Bill Volume 2 after she snatches out her remaining eye and crushes it underfoot, leaving her stuck in the narrow-halled trailer with a poisonous snake while she's thrashing about in a literal and figurative blind panic — all in the middle of the desert. She was toast.
She also "spares" Sofie Fatale after chopping off her other arm (the first was lost when fighting O-Ren) during her interrogation and hurling her down a hill, just so that she can deliver a message to Bill, and makes a point that she could do a lot more than just take her arm if Sofie doesn't cooperate.
In Serenity, Captain Mal spares the Operative's life so he can show him a message which proves that an Alliance experiment killed almost everyone on the planet Miranda and created the Reavers out of the remainder, crushing the Operative's dream of the Alliance creating a "perfect world".
Mal: "I ain't gonna kill you. Hell, I'm going to grant your greatest wish - I'm going to show you a world without sin."
300: "You there. Ephialtes. May you live forever." To the Spartans, not achieving a "beautiful death", which meant dying in battle, was a horrifying prospect for Spartans; those who died of old age didn't even get gravestones.
In The Karate Kid Part II, Mr. Miyagi tells Daniel that he let John Kreese live (after inducing Kreese to break both of his hands, delivering an Ironic Echo of Kreese's own words, and embarrassing him with a nose grab) because for a man as twisted as him, living is a worse punishment than dying.
In the recent Burton adaptation of Alice's Adventures in Wonderland, the White Queen, due to her vows not to harm any living creature, condemns her sister to spend eternity wandering the borders of Underland chained to her right-hand man, the one person she loves. Being shunned wouldn't have been so unbearable, since she thought he loved her too... until he tried to kill her, and later begs to be killed to get away from her. The only response from the White Queen is a faint smirk and the reply "But I don't owe you a kindness.". Beware the Nice Ones indeed...
Invoked and then subverted in John Ford's My Darling Clementine. After the O.K. Corral gunfight, Wyatt Earp tells Old Man Clanton (whose sons have just been killed in the fight, and who had earlier killed Earp's brother James) that he's not going to kill him: "I hope you'll live a hundred years, so you'll feel just a little of what my pa's gonna feel." Then he tells him to get on his horse and get out of town. As Clanton is departing, however, he suddenly turns to shoot Wyatt, and Wyatt's brother Morgan shoots and kills him.
In Shenandoah, Jimmy Stewart's character confronts the young Confederate soldier who's just shot and killed one of his sons after mistaking him for a Union soldier, telling him he hopes he lives a long life and has many children so that he can come to feel about them the way that Stewart does. "And then, when a man comes along and kills one of them..." he starts, before he's overcome with emotion and walks away.
Little Big Man has a scene where General Custer spares Jack Crabb's life, after Crabb attempts to kill him in his tent but loses his nerve at the last second. Crabb states in narration that this is the worst thing Custer could have done to him.
Near the end of The Departed, Costigan finally captures Sullivan, The Mole inside the police force. Sullivan begins trying to threaten and intimidate Costigan, then begins breaking down into tears and pleading with Costigan to "Just kill me". Costigan refuses, saying "I am killing you", meaning that he's intent on bringing Sullivan up on charges, thus ruining his life and forcing him to live through and experience everything that will result from that. Immediately afterwards Costigan is killed, and a couple scenes later, after getting away with everything, Sullivan receives a rather painless death.
He does much the same thing to the Big Bad of Fire Down Below, disabling his enemy with one shot instead of killing him, for much the same reasons as the above flick. No one ever accused Steven Seagal movies of an abundance of originality.
In Training Day, Ethan Hawke's character leaves Denzel Washington's character alive after their final confrontation. It might seem merciful, but Denzel owes a very large debt to the Mafiya, and Ethan took the money he was going to use to pay them off. He doesn't last long.
A lenient example - sort of - happens in The Good The Bad And The Ugly. At first it seems like Blondie is going to ride away and leave Tuco to hang himself when he eventually falls as retribution for double-crossing him. At the last minute, however, he turns, and fires his rifle, severing the rope, saying "Just like old times." Tuco is alive and has his share of the gold, but with no horse and in the middle of the desert, getting back to civilization won't be easy. (Of course, he did manage it when Blondie abandoned him at the beginning of the movie.)
In Seven there's one point where murderer John Doe has Detective Mills hurt and at gunpoint, but spares him, and later even apologizes for hurting Mills when he speaks to the officers on the phone. Instead he saves Mills for a Fate Worse than Death, which sends Mills straight into a Heroic BSOD.
In Bent, Max convinces the guards in the concentration camp to let him and Horst have a better, safer job than the other people. Taking rocks from one side of the room, and putting them in a neat pile on the other side of the room. They then have to repeat this task over and over, all day, every day. Eventually they both start going insane from this psychological torture, and start dreaming about piling rocks even in their sleep.
Bowden: "No! That would be letting you off too easy, too fast. Your words - do you remember? Well, I do. No, we're going to take good care of you. We're going to nurse you back to health. And you're strong, Cady; you're going to live a long life... in a cage! That's where you belong, and that's where you're going - and this time for life! Bang your head against the walls. Count the years... the months... the hours... until the day you rot!"
At the beginning of Hocus Pocus, Winnifred Sanderson punishes Thackery by transforming him into an immortal housecat.
Winnie: His punishment will not be to die...but to live forever with his guilt.
In the end of Ever After, Danielle saves her stepmother and stepsister from transportation to America, and almost certain death. When the queen asks her what shall be done with them instead, she simply asks "That you show them the same kindness that she showed me." That kindness would be de facto slavery.
In the biopic film Elizabeth, the eponymous queen has Walsingham expose the catholic plots to assassinate her, culminating in her ex-lover Lord Robert Dudley being exposed as one of the conspirators after she previously rejected him. He knows he is destined for execution as a traitor to the crown and begs for it, but Elizabeth decides: "I rather think to let you live; to remind me of how close I came to being weak."
Khan: I done far worse than kill you. I've hurt you, and I wish to go on... hurting you. I shall leave you as you left me, left her, marooned for all eternity at the center of a dead planet, buried alive, buried alive...
In the Harry Potter series, in the fifth film, Harry sums up why Good Is Not Soft when he refuses to help Umbridge from the Centaurs, despite her insistance that he has to save her since he's a good person;
Harry: I'm sorry Professor... but I must not tell lies.
In Highlander Endgame, Jacob Kell's goal is to make Connor MacLeod's life a living hell, killing all those close to him and keeping Connor alive until they are the last two Immortals left.
Star Trek III: The Search for Spock: For Klingons, getting captured alive is probably the worst humiliation you can visit upon them. The one remaining crew member of the Klingon ship gets the Enterprise crew to promise to kill him instead of keeping him captive. Later, Kirk orders them to lock him up. When the Klingon shouts, "But you said you would kill me!", Kirk responds: "I Lied".
Bane: You don't fear death. You welcome it. Your punishment must be more severe.
Bruce Wayne: Torture?
Bane: Yes. But not of your body. Of your soul.
Bruce Wayne: Where am I?
Bane: Home, where I learned the truth about despair, as will you. There's a reason why this prison is the worst hell on Earth: hope. Every man who has ventured here over the centuries has looked up to the light and imagined climbing to freedom. So easy. So simple. And like shipwrecked men turning to sea water from uncontrollable thirst, many have died trying. I learned here that there can be no true despair without hope. So, as I terrorize Gotham, I will feed its people hope to poison their souls. I will let them believe that they can survive so that you can watch them clambering over each other to stay in the sun. You can watch me torture a city. And then when you have truly understood the depth of your failure, we will fulfill Ra's al Ghul's destiny. We will destroy Gotham, and then, when it is done and Gotham is ashes... then you have my permission to die.
A Battle Sister in the Warhammer 40,000 novel The Bleeding Chalice refers to the villainous version of this trope: Chaos troops sparing Imperial soldiers because they'll suffer more that way, after she was spared by the "traitor" Sarpedon (who was actually sparing her because he was a good guy at heart(s) and admired her determination).
In Trooper Caffran's Day in the Limelight in Ghostmaker, his squad encounters and defeats a Khornate Chaos cult, which worships death. As a reward, he gets to execute the cult leader personally - but refuses, saying that since the cultist longs for death, keeping him alive is the real way to punish him. Gaunt agrees.
One of the short stories in Fear the Alien anthology book has a Dark Eldar Archon sparing the life of a woman who answered his question, despite her begging to die since her husband was killed. Unusually for Dark Eldar, tho, the Archon was not being intentionally cruel: he spared her life so that she may savour her agony, which the Dark Eldar (being beings who literally feed on pain and misery) would consider a good thing.
At the end of Fool's Fate, the Pale Woman's prophecies have all been thwarted and her power destroyed. She screams at Fitz to kill her, saying that her visions told her this would happen if she failed. Fitz responds that they are not in her vision of the future but his, and that she dies slowly, alone. She does.
This is advocated in The Bible. "If your enemy is hungry, give him food to eat; if he is thirsty, give him water to drink. In doing this, you will heap burning coals on his head."
In Mountains of Mourning novella Miles Vorkosigan had to judge an old woman for the killing of her "mutant" granddaughter (who only had a harelip, actually). The woman was upholding cruel traditions she'd grown up with, but executing her (per the law) would not serve any purpose other than to make people cling more tightly to the backwards traditions rather than less. Instead, Miles declared her legally dead and forbade anyone from performing traditional funerary rites for her. In her mind, and in the minds of those who would have agreed with her killing her granddaughter, this effectively destroyed her soul. It also made her legally dependent on her daughter, the mother of the child she had murdered.
In a later Miles Vorkosigan novel, Memory, his boss/mentor Illyan's biochip was sabotaged by one of Illyan's subordinates and friends, which nearly drove him insane to the point where he begged for a clean death. After they ferret out the culprit, Miles wonders if the man will commit suicide now that he's been caught, and asks Illyan if he would want to allow that.
Illyan: Dying's easy. Living's hard. Let the son of a bitch stand his court-martial. Every last eternal minute of it.
In Les Misérables, Valjean frees Inspector Javert, the man who hunted him for nearly 20 years of his life when the latter is captured and sure to be executed by La Résistance for spying on them. Valjean doesn't mean it to be cruel but for Javert it's the cruelest thing he could have done: it breaks his brain that he should owe his life to Valjean, whom he thought of only as a criminal and fugitive. The Cognitive Dissonance drives him to suicide. Borrowing a line from the musical adaptation:
Done in Animorphs to Visser One (formerly Visser Three): when he's finally captured, he's made to give up his prized Andalite host body, put on trial for his many, MANY crimes, and forced to live out the rest of his life in his natural Yeerk state (i.e. blind and helpless) imprisoned, in complete isolation, and with no chance at ever getting another host body.
In the third book Harry Potter convinced his godfather Sirius not to kill the bastard who had framed Sirius for serial homicide and condemned him to a decade of horrible imprisonment, so they could instead lock him in the same nightmarish prison Sirius had been locked in, where foul, joy-draining demons would slowly drive him into madness and death. Naturally, it backfired, but it wasn't all about vengeance, per se.
Attempted by Lysa Arryn in A Song of Ice and Fire. When her prisoner, Tyrion Lannister, wins his trial by combat, Lysa is forced to release him... so she orders him to be escorted to the Kingsroad, where he will be at the mercy of bandits.
Sansa Stark convinces Joffrey to spare Ser Dontos by appealing to his sense of cruelty, telling him it would be far harsher to make him a fool than to have him killed. It kind of comes back to haunt her later.
Arya Stark refuses to grant Sandor Clegane a Mercy Kill when he's wounded and feverish, instead riding off and leaving him to die. It's implied however that despite Sandor's atrocities she is reluctant to kill him, after all they've endured together.
In Day Watch (second book of the Night Watch series) a group of Dark Others is convicted of a serious crime and given the option between two fates: execution by hanging (as opposed to the more severe dematerialisation) or being allowed to live in return for never using their powers again and living a normal human lifespan. When they choose the latter option, Gesar (head of the Light One delegation) is asked if he has any opinion, and he reluctantly recommends that their sentence be commuted to permission to perform extremely minor magic, which is granted. One of the Day Watch witnesses notes that, in the long term, this is even crueler than being killed or having no magic at all, as using incredibly weak spells will act as a constant reminder of the power they truly have but can never use.
Featured a lot in the Discworld witch books, actually. In Witches Abroad, Lady Lilith locking the witches in a dungeon instead of having them executed is described as this.
The Elf Queen tries this on Granny Weatherwax in Lords and Ladies, describing how she'll drive Granny insane, reduced to looking through scraps while remaining aware of how the villagers see her. Too bad Granny already knows what the villagers think of her, and doesn't care.
In Maskerade, a band of muggers threaten Granny Weatherwax, only to injure themselves in an encounter with the Ankh-Morpork Opera House's famous Phantom. Granny decides to take pity on them by stitching up their self-inflicted wounds... with a blunt needle.
The whole philosophy runs like this: if you kill your foe, your foe is dead and that's that. If you beat your foe, but let them live, then your foe is beat and knows they've been beat, and they'll know it for the rest of their life, and there's no point in beating a foe if they won't be around to know they've been beat afterward.
Magnificent Bastard Vetinari knows usurping rulers like to employ this trope and plans for it. "Never build a dungeon you wouldn't be happy to spend the night in yourself." Said dungeon has locks and bolts on the inside of the door, secret stash of food, keys and other things. Also, room service (intelligent magically-mutated rats).
In Dune: House Harkonnen, Duke Leto invokes this trope on a man who was involved with the death of Leto's son (and is very remorseful about it, to the point that he is considering suicide):
Leto: I sentence you... to live.
In the Star Wars Expanded Universe, when Boba Fett escapes from the sarlacc's stomach, he considers killing it, but leaves. The sarlacc asks him why, and he says that leaving it alone in the desert, immobile and depending on creatures falling into its mouth every few years for food, will be a more fitting revenge.
I Have No Mouth and I Must Scream is very, very much about this: The antagonist is an insane, sentient supercomputer who has brutally murdered the entire population of Earth, save for five people he keeps indefinitely alive inside his own systems and tortures for his own amusement. And when four of these five people find a way out, the supercomputer punishes the remaining survivor by making him incapable of suicide and altering his perception of time. The computer game adaptation expands on the supercomputer's motivations, by explaining that in becoming sentient, he was driven mad by only being able to use his vast intellect to kill others.
After Mr. Wickham runs off with Lydia in Pride and Prejudice and Zombies, Mr. Darcy tracks them down and bribes Wickham into marrying Lydia and going into the priesthood on the condition that Darcy gets to beat the crap out of Wickham. The punishment is threefold: Wickham is trapped for life with the most annoying person in the entire P&P&Z universe, he has to give up gambling and seducing women, and he can't run away from any of this because he can't move under his own power. Considering that the Bennett family probably would have just killed him, this punishment is somewhat more fitting.
In one of the Horrible Histories books, Terry Deary writes an account of Lambert Simnel, a peasant boy who was chosen to be the figurehead of a rebellion against Henry VII because he resembled the Earl of Warwick. Henry crushed the rebellion and made Simnel one of his servants in a display of Pragmatic Villainy. In Deary's account, Simnel is left shellshocked by watching the rebels being slaughtered, and writes: 'Cruel Henry had the real Earl of Warwick put to death, but cruellest of all, he sentenced me to live'.
Used in one of the John Carter of Mars books. A minor bad guy has just been caught rigging a duel to put John Carter at a disadvantage, and the jeddak orders said bad guy to duel Carter. Carter simply carves an X in the guy's face, then disarms him and declares that he's satisfied because living with that scar is a Fate Worse than Death.
The Scarlet Pimpernel deliberately invokes this in the sequel Sir Percy Hits Back when he tells his Arch-Enemy Chauvelin that he finally has his chance for revenge. Chauvelin naturally assumes that the hero intends to let Chauvelin's daughter be executed but find out at the end that Sir Percy's "way of hitting back" is to save his daughter and spare his life. No! Anything but that!
In Roger Zelazny's Forever After, Gar Quithnick uses a nerve strike on a deposed villain that will kill him the instant he holds himself superior to another person, although he can still live a long life of humility.
"You said 'God is cruel' the way a person who's lived his whole life on Tahiti might say 'Snow is cold.' You knew, but you didn't understand. Do you know how cruel your God can be, David? How fantastically cruel? Sometimes he makes us live."
Kvothe himself does this to the leader of a group of thieves and rapists pretending to be Edema Ruh. The rest of them he simply kills, but he wounds the leader fatally in the stomach and leaves him alone to die by inches, leaving behind a water skin only so that dying of thirst won't end his pain before the wound kills him.
Honor Harrington: When pragmatic politics requires that she can't simply have them offed, or even tried, Queen Elizabeth III of Manticore forces the two conspirators most responsible for her father's death into exile on newly-annexed and quite primitive Basilisk, away from their political power bases, and allows the third to move to Sphinx and perhaps find a treecat to adopt her. Being empathic, every treecat will know she's a traitor.
If you've pissed off Harry Dresden and he doesn't kill you, it's because he's making sure you really suffer. On one occasion, a man possessed by a Fallen Angel "agreed" to repent before Knights of the Cross - since technically, getting such repentance is their job, it gave him immunity from them, but not from Harry. This comes back to bite him later.
Mab keeps giving Harry the option of giving her disgraced Winter Knight a Mercy Kill. Harry says he doesn't deserve it. Harry does eventually kill him but he's only doing it because he needs to claim the Mantle of the Winter Knight. He refuses to consider it mercy.
Wizards in the Sword of Truth like doing this. Zoranders and Rahls are especially well-known for it.
Implied in Mary Shelly's Frankenstein. After Frankenstein's death, the monster himself explains how letting the monster live would have been a more satisfying revenge than killing it outright, since forcing it to live alone and in guilt of its crimes would be torturous.
In one episode, a hypochondriac sells his soul to the devil for immortality. He starts thrill-seeking, but his wife dies trying to stop him from jumping off a building. He's convicted of murder and tells his lawyer to get him sentenced to the electric chair, but his lawyer manages to talk the judge down to life in prison instead..
The end of the episode "The Family of Blood": "We wanted to live forever.So the Doctor made sure that we did." In fact, an earlier warning that he may be forced to kill the family is revealed to actually have been an offer of kindness in comparison (though what he had really been pushing for up to that point was to help the whole family find a planet they can live on peacefully without harming any intelligent creatures).
In a later episode, "I forgive you" was almost certainly as devastating to its target, but the Doctor probably didn't mean it to be. But then, what could possibly be more devastating to the Master than being at someone's mercy, i.e., being under another's mastery? So much so that when Lucy shoots him, he REFUSES to regenerate, despite having spent the entire classic series descending to progressively lower depths just to keep himself alive.
Also, in "A Good Man Goes To War", he shows his cruel mercy by making the man who plotted to kill instead get known as "Colonel Run Away".
The Doctor: No. Colonel Manton, I want you to tell your men "run away."
Colonel Manton: What?
The Doctor: Those words. "Run away." I want you to be famous for those exact words. I want people to call you Colonel Runaway. (getting angrier) I want children laughing outside your door, 'cause they've found the house of Colonel Runaway. And when people come to you and ask if trying to get to me through the people I love! (he composes himself)...is in any way a good idea, I want you to tell them your name. Look, I'm angry, that's new. I'm not really sure what's going to happen now.
Madame Kovarian: The anger of a good man is not a problem. Good men have too many rules.
The Doctor: Good men don't need rules. Today is not the day to find out why I have so many.
Madame Kovarian: Give the order. Give the order, Colonel Runaway
The War Doctor had every intention of dying with the Gallifreyans and Daleks when he activated the Moment, a sentient superweapon, as he believed he didn't deserve to live. The Moment understood just how much this trope would hurt him.
The Moment: Then that's your punishment. If you do this, if you kill them all, then that's the consequence. You. Live.
A Law & Order episode ended with the wife of a man who blew up a helicopter (killing all six passengers, including his wife's alleged paramour) begging the court to not use the death penalty. When it was revealed that the wife was the Chessmaster who set the whole thing in motion by faking the affair, the attorneys asked why she begged for mercy for her husband. The answer: she wanted him to live a long life knowing he was powerless and trapped.
Fred attempted this when she found out exactly who sent her to Pylea, and opened a portal to a far worse hell dimension. However, Gunn couldn't bear to see her do that to somebody else, so he ran up and broke the man's neck before he could get sucked in.
Angel himself spent many years as a soulless vampire committing countless atrocities including killing everyone in his village including his own sister. After torturing and killing the favorite daughter of a tribe of Kalderash Gypsies, they curse him by restoring his human soul, thus afflicting him with a conscience and condemning him to an eternity of remorse for the crimes he has committed.
Later, Connor locked Angel in a steel coffin and dropping him in the sea, knowing that he would not die, but starve and go mad.
D'Hoffryn pulls one of these on Anya in an episode of Buffy. Overwhelmed with guilt over slaughtering a fraternity for a vengeance wish, Anya begs D'Hoffryn to undo it. He tells her the price is the life of a vengeance demon; to atone for her actions, she is all too happy to accept death. He then summons Anya's friend Halfrek and kills her instead.
D'Hoffryn: Haven't I taught you anything, Anya? Never go for the kill when you can go for the pain.
IN the episode "The Colonel", during a flashback set in World War I Immortal Simon Killian ignores an order that the war has ended and orders his men to attack, resulting in the unnecessary deaths of many soldiers on both sides. At his trial, he is initially convicted and sentenced to death by firing squad, but Duncan testifies that Killian was insane at the time and didn't deserve execution. Killian is sentenced to life in prison, spending 70 years locked up.
In another episode, the crew of a ship mutinies against their uncaring captain, an Immortal. Duncan convinces the crew to leave him on a deserted island, rather than shoot him. When the captain pleaded with Duncan not to leave him there, Duncan told him he brought it on himself and to be thankful he still had his head attached. The Immortal captain spent over 100 years on that island, dying of hunger and thirst every few days, only to revive.
Captain Kirk and company at one point find themselves trapped with the infamous Harry Mudd, an Affably Evil fraudster. The Enterprise crew works together with the villain to escape the android-run prison that they are trapped in, but in the end Kirk decides to leave Mudd behind. Mudd is left to enjoy a life of luxury, but is also left with at least 500 androids— all of which have been programmed to mimic his overbearing, nagging wife (and ignore his override commands!).
Forcing Cyrano Jones to pick up every single tribble on K-7 (a task estimated by Spock to take 17.9 years), instead of arresting him for trial, is a form of Cruel Mercy on Kirk's part. Especially when you consider there's nothing to stop the tribbles breeding...
Kirk had told him that the sentence he would have received for the crime would have been 20 years, so he considered it a better option. Still, the problem with them continuing to breed was a concern that no-one mentioned.
Cultural differences resulted in Cruel Mercy to Worf's brother Kurn in the Star Trek: Deep Space Nine episode "Sons of Mogh". With their family dishonored in the eyes of the Empire, Kurn seeks Worf out to give him his honor back... by killing Kurn in a specific ritual. When Dax puts the pieces together (the identity of the Klingon that recently arrived; Worf's belligerence toward Quark over acquiring a specific type of Klingon incense), she arrives just after Worf has struck with the ritual blade, but is in time to have Kurn transported to the infirmary and save him. Denied the restoration of his honor (especially since Sisko threatened Worf not to try it again), Kurn suffers a Fate Worse than Death for a Klingon, and slips into a deeper depression, turning suicidal... until Worf decides to provide him with a new identity, and have Kurn's memory wiped, so that he can start his life as a Klingon anew.
In the Star Trek: The Next Generation episode "Too Short A Season", a now-aged admiral returns to negotiate with a hostage-taker he had previously betrayed years ago—the terrorist wanted weapons, but the admiral gave them to both him and his enemies to preserve the balance. The admiral is taking illegal drugs that make him de-age, but eventually cause incredible pain and death. When they finally meet, the terrorist initially wants to kill the admiral with one of his own smuggled weapons for poetic justice, but then decides a better revenge is to leave him to live in the pain caused by his drugs.
In the fifth season, Peter and Hiro don't kill Samuel Sullivan. They reveal his crimes to his fellow super carnies and teleport them away, taking away Samuel's surrogate family and powers in one stroke. Samuel has a Villainous Breakdown as he stumbles around the empty carnival, alone and powerless.
Midway through the final season, popular supporting cast character Ronnie Gardocki gives a speech about how killing turncoat murderer Shane Vendrell would be too merciful and would be more content with him rotting in jail for the rest of his life. The irony fairy strikes Ronnie at the end of the series as he is arrested and facing possibly spending the rest of his life in jail. A nasty bit of subversion, given that Ronnie survived countless injuries that would have killed lesser mauve/red-shirt characters over the course of the series, let alone him being the only subordinate of Vic Mackey's to survive the end of the series alive.
Vic Mackey's final fate as well could be described as "cruel mercy"; made to face the fact that he turned his protégé into a man who murdered his pregnant wife and young son, forced to watch his most loyal friend arrested (with his betrayal of Ronnie shoved into both men's faces for added "fuck-you"-ness), and then ordered out of the police precinct, now knowing that every one of his sins are now public knowledge amongst the rank and file police officers who used to look to Vic as the precinct's resident Alpha Male. Vic Mackey was given immunity for his numerous and varied crimes, and got a nice cushy contract working for ICE to boot. However, Agent Murray, in her capacity as Mackey's Literal Genie, tells him that he's not going to be out on the street busting skulls like he used to; he's going to be sitting at his desk, with its sterile surroundings and bad lighting, doing paperwork for his entire tenure. Noncompliance means dissolution of his immunity agreement, and off he'll go to prison. And once said tenure is over, he'll be kicked out and never be allowed to work in law enforcement again. Some familiar with Mackey's character would see this as his own personal hell. This is open to interpretation, however, as the last scene of the series is Vic strapping on his pistol and heading out into the night, suggesting that he will somehow find a way to continue being who and what he is.
In Robin Hood, Robin spares Gisborne's life after he has killed Marian, the woman they both loved, and Robin's wife. Gisborne begs Robin to end his life; instead Robin spares him and forces him to live with his guilt (though by the next episode Guy is terrorising the village of Locksley and ends up killing the new regular's kid brother, so letting him live probably wasn't such a good idea after all).
Mal: I bet. It would be humiliating, having to lie there while the better man refuses to spill your blood. Mercy is the mark of a great man. * stab* Guess I'm just a good man. * stab* Well, I'm alright. * throws down his sword and walks away from his more-wounded-than-necessary opponent*
Blakes Seven: Towards the end of Season 2, Blake calmly refuses to kill his nemesis Travis, now a crippled fugitive. Considering what happens in the season finale, this turns out to be a pretty major head against wall moment, something both Jenna and Travis point out in the scene itself.
A villainous example is seen in the Merlin TV miniseries. After he turns against her, Mab removes Frik's powers, but doesn't kill him, instead leaving him to wander the world in his misery, not a magical being but not quite human either. Luckily for him, he turns out to be quite happy as a human.
There's a particularly vicious example in La Reina del Sur where Teresa, a drug trafficker in Spain, captures and tortures one of her many enemies, a French heroin trafficker who also uses the drug to keep women high and under his control in his brothel. She has him savagely beat with a bat to the point where his spinal cord is damaged beyond repair, yet she leaves him alive so that he can "drag himself at the feet of others like the animal that he is," as Teresa stated (she had major issues against someone using drugs to force women into prostitution). He is killed in the following episode for telling the cops about it, though.
At the end of Season 2, John is strapped to an operating table to remove the neural chip Scorpius had implanted in his brain. Partway through, Scorpius comes in, incapacitates the doctor, takes the chip, and... lets John live, strapped to the table and unable to speak. It's especially fitting given what drives Scorpius.
Scorpius: I condemn you John Crichton... to live. So that your thirst for unfulfilled revenge will consume you! Goodbye.
In the Season 4 episode "Mental as Anything" Macton (the man who killed Dargo's wife) interrupts Dargo's session in a Mental World in an attempt to break his mind. Luckliy, Dargo prevails and ends up breaking Macton instead. When asked why he didn't kill Macton, Dargo can only say he wasn't enlightened enough to give the man a Mercy Kill.
True Blood. Eric wanted to leave Russell in the sun to burn, until he had a vision of Godric and decided to spare Russell. By burying him in concrete the following night. Naturally, his vision of Godric does not approve.
Used quite often on Burn Notice. Though some of his opponents do get killed as a result of Michael Weston's machinations, just as often they are left alive, in the burning wreckage of their lives, holding the match as the police sirens close in.
Hotch explicitly cites this idea on Criminal Minds when he explains to Haley why he doesn't think that Foyet will make an explicit attempt on his life.
The perp in the CSI: Crime Scene Investigation episode "Living Legend" turns out to be Mickey Dunn, a legendary mob boss thought dead for decades going on a Roaring Rampage of Revenge on the people who tried to kill him. The reason why he waited this long is revealed when he goes into cardiac arrest: the bullet in his chest moved and he was told that he only had a week to live. When he wakes up, he brags about how this will go public and his legend will be revived only for Catherine to show him the bullet: the hospital doctors (much more competent than "mob doctors") removed the bullet with no problems, and estimate Dunn now has about 20 years to live, all of which he will spend in a prison filled with a generation of criminals who don't know who he is and eventually fade to obscurity.
On Luther, the title character gives this to Ian Reed, refusing to kill him and insisting he is punished for his crimes despite (or perhaps because of) the fact that he's transparently trying to commit Suicide by Cop. He's very unhappy when Alice Morgan then decides just to kill him anyway.
Parodied in Blackadder Goes Forth. Blackadder and Baldrick crash behind German lines and are captured during World War I. The Red Baron tells them that rather than have them shot, they're going to be sent to a convent to teach home economics to girls. "For a man of action such as yourself, the humiliation will be unbearable!" The punishment doesn't seem like such a bad thing to Blackadder.
Gus Fring from Breaking Bad does this to Hector Salamanca, keeping him alive and visiting him every time he kills someone related to Salamanca. Made worse by the fact that Salamanca can only move his finger.
Captain Horatio Hornblower R.N.: Horatio attempted this on Simpson, after given a free shot at him when he cheated in their duel. After hearing Simpson beg for his life, Horatio spares him, declaring that he's not worth the gunpowder. Ultimately subverted in that Captain Pellew disagreed, and also didn't take kindly to Simpson trying to backstab Horatio after that declaration.
In Once Upon a Time, Snow White is in a major Heroic BSOD and shows signs of being a Death Seeker. She goes to Regina and asks her to end the feud (and her misery) and just killer her. Regina is at first happy to oblige, but then notices a dark spot in Snow's heart. Regina gleefully explains that that spot will grow, and darkness and evil will consume her. It will destroy her and her family. So Regina decides to let Snow live, despite her now begging for death, knowing that this will be her revenge.
Defiance: In "The Serpent's Egg", Irisa lets Daigo live despite him being responsible for the abuse she suffered as a child, because being forced to live a normal life is far greater a punishment than any torture or execution she could give him.
In the episode of Are You Afraid of the Dark? called "The Tale of Cutter's Treasure," a boy’s little brother is kidnapped by the ghost of Jonas Cutter, a pirate captain cursed by the boys’ grandfather to guard a cave filled with treasure but never be able use it. He rescues his brother, and defeats Cutter in battle with a magic dagger, but he quickly realizes that using the dagger on Cutter would put his his soul to rest. Rather than allow Cutter to be free from his curse he breaks the dagger and abandons him in the cave,leaving him trapped guarding his treasure, alone forever.
And once again in Shakespeare's Cymbeline by Posthumous Leonatus to Iachmo who had just confessed to masterminding a plot which caused Posthumous to order his wife murdered.
"The power that I have on you is, to spare you; The malice towards you to forgive you: live, And deal with others better. "
In William Shakespeare's Measure for Measure, the Duke does not kill Lucio as threatened, but forces him to marry the whore who bore his child. "Marrying a punk, my lord," Lucio laments, "is pressing to death, whipping, and hanging."
Depending on how you interupt it, the Big Bad Angelo suffers this as well. The Duke doesn't have him killed, but forces him to wed a wife he didn't want and live after being revealed publically for his crimes. His original plan was to have him marry her and then be killed, but ultimately changes his mind.
In William Shakespeare's The Merchant of Venice, Antonio insists on Shylock, a Jew, converting to Christianity as punishment for what he's done. For a Jew, that's... let's just say bad. In Yiddish, the word for "Jew", "yid", is used as a synonym for "person". As a former Jew, he'd be neither accepted by the Jewish community nor the Christian one. And as what's a pitiful parting shot in comparison, Antonio takes some of his money and forces him to bequeath his estate to his runaway daughter and son-in-law in his will.
Even worse, in Shakespeare's time, this would have been considered a happy ending. The Jew gets to be saved, right? It was not until much later that productions started to focus on the negative consequences of converting.
Yet another Shakespeare example: In Romeo and Juliet, after being sentenced to exile instead of death, Romeo, in his usual Emo Teen manner, declares exile to be a Fate Worse than Death because it means separation from Juliet, and threatens to kill himself. Friar Lawrence, in the play's longest speech, proceeds to chew him out over all the Wangsting he's been doing.
A common habit among the Infernal Exalted. Indeed, there's a Kimbery charm which ensures this is the only kind of mercy you can show without spending willpower.
As many stories in the Ravenloft setting have proven, may the gods help you if you to try to cheat, con, steal from, or harm the Vistani. They are notorious for inflicting dark and horrible curses on anyone who does, and victim of such often wish they were never born.
This happens in the Golden Ending of Call Of Duty Black Ops 2. If the player spares Menendez, he doesn't get martyred for Cordis Die like he wanted to. In addition, all of his plans unravel, and he has to watch the people who did it from inside of his cell.
In the trailer for Portal 2's co-op mode, GLaDOS provides a voice-over that ends, "Do not disappoint me..." Beat "...or I'll make you wish you could die!"
Disgaea 3: Absence of Justice: In the 'normal' ending of after defeating Super Hero Aurum, who orchestrated everything that happened in the game, the defeated boss asks Mao to kill him. Mao refuses, and instead drags Aurum home to his lab to 'experiment' on him, presumably to unlock the secret of his One-Winged Angel transformation. You see him briefly during the credit-roll, and he looks... decidedly uncomfortable. This is particularly amusing in that Aurum THOUGHT he was performing a Xanatos-Gambit - if he had defeated Mao, he would have been famous and revered throughout the world as the hero who slew The Overlord, and if he lost, he got the glorious death he'd always wanted... shame it didn't work out that way, huh?
Played with in the original, where Flonne wants Laharl to throw a fight against the ghost of a hero so that he can rest in peace after defeating a Demon Overlord, but Laharl refuses and fights with everything he has, defeating the ghost. The ghost then thanks Laharl for the battle, pointing out that the only heroic death is to fall against a mighty opponent; Flonne was unknowingly promoting Cruel Mercy, while Laharl was being mercifully cruel.
Disgaea 4 gives us Nemo, an Omnicidal Maniac who firmly believes Humans Are the Real Monsters and seeks to wipe out Earth (which will mean the end of Celestia and the Netherworld as well). When he finally discovers that Artina, the one example of Incorruptible Pure Pureness he ever encountered in this Crapsack World, is "alive" as an angel, he relents and tries to pull a Redemption Equals Death. Specifically, this will mean the destruction of his soul. The heroes decide that this is not sufficient punishment for his crimes, and instead give him a normal death so that he will be reincarnated as a Prinny and be forced to work off his karmic debt. They then cheerfully list the horrible labors they will have him endure for eons. In a mild subversion, Nemo accepts this and the end credits show him as a Prinny looking up at the Red Moon (signifying his eventual reincarnation).
Near the end of Dragon Quest VIII, Angelo saves Marcello from a Disney Villain Death. Given that he had just given a massive "The Reason You Suck" Speech to a crowded amphitheater that veered into Evil Gloating, then was possessed by Rhapthrone and resurrected the demon's body in front of said crowd, leaving his ambition, reputation and everything he'd spent his entire life working for in tatters... yeah, death would've been kinder. Getting saved by the half-brother he despised was just another kick in the side at that point.
In Starcraft, Kerrigan exhibits this on Zeratul after he kills his Matriarch who demonstrated that she was Kerri's thrall.
Kerrigan: "I said you are free to go. I've already taken your honor. I'll let you live because I know that from now on your every waking moment will be torture. You'll never be able to forgive yourself for what I've forced you to do. And that, Zeratul, is a better revenge than I could have ever dreamed of."
She also showed cruel mercy to Mengsk:
Kerrigan: "I think I'll leave you here, Arcturus, among the ashes of your precious Dominion. I want you to live to see me rise to power. And I want you to remember, in your most private moments, that it was you who set me loose in the first place."
As Starcraft II showed, however, that part really didn't stick: Four years later, the Dominion has become the dominant power in the Korpulu sector and Kerrigan is nowhere to be found. The campaign ends with Mengsk almost succeeding at 'fixing' his mistake. In Heart Of The Swarm, Kerrigan has also learned from this and just kills Mengsk.
Briefly mentioned in Titan Quest when the Yellow Emperor reveals that the Telkines are rampaging around to free Typhon, strongest of the Titans. The gods banished all other Titans after defeating them, but bound Typhon in nigh-unbreakable chains beneath a mountain so for all eternity he would be chained to what he desired most but could never have.
Arguably, you can pull this on two of the Jedi Masters you're trying to find, too. Let's see, Vrook. You're on this rock that hates Jedi, but makes an exception for me because I saved the place and you didn't. Have fun. Oh, Zez-Kai, you're a broken coward living in a Wretched Hive, surrounded by every Crapsack World trope in existence and you can't manage to pick up your lightsaber and do a thing about it while I did. I'm getting stronger and will kick the Sith's arse while you sit and mope. Meditate on that for a while and get back to me.
According to Ryusei Date, this trope is the true reason behind the 'Mercy' Spirit Command on the Super Robot Wars series, which leaves the target with 10 HP if the next attack would destroy it.
In the canon ending of Drakengard, Caim doesn't kill Manah after defeating her, instead opting to personally drag her around the entire country and tell everyone that they meet that everything that has happened was entirely her fault (well, figuratively 'telling': Caim's mute. Presumably he uses Sign Language, or 'interpretive brutal murder'). Caim, being Caim, is making a traumatized formerly-possessed 6-year-old with abandonment issues walk from village to village in the cold and the rain, just so that everybody she meets will hate her, and this is in character for him. In the end, she stabs him in the eye and jumps off a cliff to escape. When they meet again in the sequel, she utterly freaks out at the sight of him.
In Grand Theft Auto IV, you can do this to Darko Brevic, the man who betrayed Niko's old army unit. When Niko meets him, he is a drug addicted wreck, confesses to having sold out his unit's lives for a mere $1000 dollars in order to fuel his drug addiction and begs Niko to kill him. The player is thus given a choice: if Niko shoots Darko, the latter thanks him and the former ends up not feeling any better. If Niko spares him, he remarks that letting Darko live with his addiction and guilt is the bigger punishment and Darko utterly loses it. Ironically, if the player chooses to spare Darko, Bernie (the other survivor of Darko's treachery) will call Niko congratulating him for having overcome his desire for revenge.
In Neverwinter Nights: Hordes of the Underdark, if you shell out the absurd amount of money for Mephistopheles'sTrue Name, you not only get to skip the final boss fight, you can bind him to your service afterwards - including the option to force him to serve as a chambermaid in an inn for all eternity.
Deconstructed in The tale of Elwin and Shaera. The Hero defeats Lord Harke, then despite all of his crimes, spares him and locks him up, but not before delivering a long speech about how he's been humiliated and broken. Harke then somehow gets the guards to send false news of Elwin's death to Shaera, knowing that she will commit suicide. It didn't work, but it has proven that Harke is just as dangerous as a prisoner as he was with an army behind him.
In The Force Unleashed, Starkiller spares the life of Maris Brood after defeating her. Senator Bail Organa protests, but Starkiller says that she isn't free, the memories of what she had done will haunt her forever.
Baine Bloodhoof inflicts this in the World of WarcraftExpanded Universe novel The Shattering Prelude to Cataclysm. Baine wants to take bloody vengeance against Magatha Grimtotem ( Who is 90% responsible for the death of his father Cairne) and Garrosh Hellscream (Duped into being the other 10%). However, he also knows perfectly well that doing so will only cause division and civil war. Instead, upon defeating Magatha's attempt at a Grimtotem coup, he personally smashes her Shamanistic totems (an affront to the elements that would take a great deal of apology and abasement for Magatha to be forgiven for) after offering full pardons to the quarter or so of Grimtotem Tauren who would swear allegiance to the Horde. As for Garrosh, he puts aside Garrosh's role in events because the Tauren need the protection the Horde can offer.
The end of the last mission in Advance Wars: Dual Strike has something like this. If the player chooses "Yes" when Jake has to kill Von Bolt, Jake is handed a gun from Hawke, who would have shot him himself if Jake couldn't bring himself to (if the player chooses "No"). Jake doesn't hesitate, and shoots Von Bolt's chair, which was what was about to revive the Grand Bolt the good guys defeated earlier. When asked by Von Bolt why he didn't kill him, Jake stated that he didn't want him dead while everyone else cleaned up his mess.
Jake: Welcome to natural selection, chump!
In Fallout: New Vegas, Cass' companion quest involves taking revenge on two groups of people who wiped out her caravan. Cass initially wants to take a direct, violent approach, but you can instead offer to uncover evidence of the conspiracy and pass it along to the NCR. Though Cass is initially disappointed, she'll decide that the NCR's legal procedures will do more harm to her enemies than a faceful of buckshot ever could.
At the end of the Honest Hearts DLC, you'll get to help decide what the vengeful Joshua Graham does with his enemy, White Legs warchief Salt-Upon-Wounds, after crushing the rest of his tribe. Graham is all too happy to execute the tribal for his crimes (which include butchering Graham's hometown), but if your Speech skill is high enough you can exorcise his inner demons and bring some measure of peace to his soul by convincing him to let Salt-Upon-Wounds go. The ending narration reveals that despite their leader's survival, the White Legs never recover from their defeat, abandoning him and leaving him a sad, pathetic wreck of a man.
It's easy to overlook, but if you read the terminals left at the H&H Tools building and pay attention to the game's backstory, you can see that Mr. House did this. He was cheated out of the family hardware business by his half-brother, but started his own robotics company and became one of the most powerful industrialists on the planet. House all but took over Pre-War Vegas and dismantled the company that was his birthright on the stock market... except for that last store on the outskirts of Las Vegas, so that his half-brother would be around to see how successful House was. From the building's log entries, it's clear the experience drove him quite mad.
According to Mr. House, sparing General Oliver in an Independent Vegas ending either with House or you in charge counts as this. He will be forced to go back west humiliated and empty-handed as a scapegoat for leading thousands of soldiers to their deaths in an unpopular war with his chance at a political career completely destroyed. House even calculates a probability of him committing suicide from it all. The same goes for President Kimball if he's still alive, though House notes a much smaller chance of suicide.
Near the end of Star Wars: Bounty Hunter, Jango Fett faces down his arch-nemesis, Montross. Aside from doggedly attempting to kill Fett and steal bounties from him, Montross was personally responsible for the deaths of both Fett's foster figure and a later mother figure. After Fett beats Montross in their final duel, the defeated man gasps that he deserves a better death than this. So Fett leaves him alive, ignoring his pleas that Jango finish him, and Montross is subsequently given the extremely ignominious death of being torn apart by feral cultists.
Subverted in Dawn of War: Dark Crusade: Eliphas the Inheritor is confronted by a daemon who blows off his attempts to place the blame on his followers but instead of torturing him in good-old Chaos fashion, simply kills him outright.
In Mass Effect 2, Archangel's (AKA Garrus) loyalty mission involves hunting down The Mole who betrayed his squad; not only killing all ten of them, but also horribly scarring Archangel in the process. When you get to him you have the option of letting Archangel shoot him with a sniper rifle from a distance, or talking to him. If you do so he reveals that he is wracked with guilt for what he did. "I don't eat. I don't sleep. All I see are their faces, staring at me, accusing me. Some days... some days I think about just ending it all." Since it's that kind of game, you can convince Archangel to spare him — or take the more merciful option, and end his suffering.
The Mole did not cause Archangel's scars - at least not directly - since Archangel was hit by a missile from an attack aircraft. Paragon Shepard, who is an extreme Magnetic Hero who inspires others to do what's right, convinces Archangel with a mix of this trope and reminding Archangel that, though a Cowboy Cop turned Vigilante Man, he's still a good person. Avoiding the Mole's death is always a Paragon act and after being given a second chance, the mole will turn himself over to C-Sec in an attempt to atone for his actions.
There's an incident in Jacob's loyalty mission as well: you find Jacob's father shipwrecked on a planet with eventually deadly vegetation having set himself up with a harem of partially brain-damaged women from his crew (and besieged by the hyper-aggressive brain-damaged men thereof). The Paragon path has you bring him back to stand trial. The Neutral option is to let him go... having destroyed his camp's defences on the way in, so the feral crewmen can tear him apart. The Renegade option has you leave him, while Jacob hands him a mostly empty pistol.
Aside from this, there was an instance in the Mass Effect 1 DLC ''Bring Down the Sky" that allowed something similar. If you opt to let some hostages die in order to capture batarian terrorist Balak, you can either kill him outright or spare him. Doing the latter means taking him to the planet he'd tried to destroy to stand trial...which, incidentally, was where the hostages came from.
In Mass Effect 3, a sidequest revolves around a batarian terrorist (not Balak) who committed a variety of destructive acts in revenge for Shepard wiping out a batarian star system in the "Arrival" DLC of the previous game. Badly wounded from an attack on the Citadel by Cerberus, he lies in the hospital of the refugee camp, and asks you to Mercy Kill him. Shepard can either turn off his life support, or invoke this trope and call the nurse to come to his "aid".
Near the end of the first Baldur's Gate, with about three battles left in the game, you can meet Sarevok's mentor, cast aside and too injured to move. He expected to die in Sarevok's ascension to godhood and go down in history as its architect, but you have the option to leave him alive to watch his plans crumble and eventually die in obscurity (without the option to surrender).
In Assassins Creed II, Ezio does this to Rodrigo Borgia, the man behind the conspiracy that killed his father and brothers as a youth. At first Ezio sought revenge by fighting the Templars and dismantling Rodrigo's plans over the course of twenty years, only for him to go into hiding and eventually resurface as Pope Alexander VI, vested with virtually unlimited political and religious power to help the Templars further consolidate their control over Europe. Not that this stops Ezio, though, as he decides to take the fight to the Vatican and try to publicly assassinate Rodrigo, culminating in a fistfight following a chase, which Ezio won. However, instead of killing him, Ezio leaves Rodrigo alone, humiliated just as ultimate victory was within reach. Even as Rodrigo pleas to end his misery, now that he has nothing to live for, Ezio states that killing him won't bring back his family and innocence, instead letting him waste away in despair, knowing that the Piece of Eden hidden in his papal staff refused to allow him to open the Vault, but it did for Ezio. Come Brotherhood the it got worse for Rodrigo, as his role became nothing more than a figurehead for his son Cesare. Finally, when Cesare kills him (to prevent his role from influencing opposition to his cause), it was Ezio, of all people, who comes to comfort him in his dying moments, and this played as the climax of Ezio's Character Development, showing how he has transcended his desire for vengeance, having decided that everything he does, however bloody, will always be for the greater good.
In Dragon Age II, there is a way to do this to Anders. He fully expects to be executed and die as a martyr after blowing up the Chantry and enticing a full-on civil war between the Templars and Mages, and if released from custody will try to die in battle anyway if you side with the Templars. But if the Champion has a full Rivalry meter with him, s/he can convince Anders that he must atone for what he did, freeing him and keeping him in the party while you help the Templars exterminate every mage in the tower. Siding with the mages makes the mercy less cruel, but the "martyrdom would be the easy way out" aspect is still there. Writer Jennifer Hepler stated in an interview that she believed this fate would be "poetic justice".
Dragon Age: Origins itself allows you to do this to several characters, to include Sten (though the option is less about outright killing him, and more about leaving him in his cage to die later), Jowan, Zevran (who enters into a "service contract" with you afterwards), and Loghain, in exchange for him serving you and the Grey Wardens, no less. There are other potential instances, such as Branka, though the cruelness of them comes down to YMMV.
In Alpha Protocol Mike has the option to spare whoever the final boss turns out to be, knowing they'll be dragged through courtroom after courtroom for the rest of their lives, watching while their empire crumbles.
Dishonored has been billed as a game about assassination in which you don't actually have to kill anyone. You can do a full pacifist run, but the targets still need to be "neutralized" in some way or another. There's a non-lethal option for dealing with each individual target, which is often a Fate Worse than Death and possibly quite ironic.
High Overseer Thaddeus Campbell: Branding him with the heretic sign of his own religious order, rendering him into a social pariah. And then he catches The Plague.
Morgan and Custis Pendleton: Arranging a criminal to disfigure them and put them to work in their own slave mines.
In Hitman: Absolution after interrogating Lenny Dexter, 47 has to deal with him in some way. While he's given various different ways to kill him, the easiest and perhaps cruelest way is to simply drive away and leave him in the middle of the desert, letting the heat and the vultures do his job for him.
In Bioshock Infiniteyou have the choice on whether or not to kill Cornelius Slate. If you spare him, Booker remarks it "was no mercy" since Comstock's men will arrive any second and drag him off for Cold-Blooded Torture. Sure enough, if he lives, you find him in a cell, completely catatonic and broken.
Horribly/Hilariously Subverted in Schlock Mercenary after Kevyn captures an alien warlord who had just executed one of his squad members simply to test a theory and was about to do the same to his Love Interest before he intervened. Rather than take his revenge on the warlord ("I know he murdered our friend, but [revenge] will take you into a very dark place, Nick"), he opts to turn him in to the proper authorities... who will then kill him and eat hima little bit at a time!
Nick: Your place sounds darker, sir.
Kevyn: It has the advantage of being legal.
Thaco in Goblinsdestroyed Dellyn Goblinslayer's carefully-constructed legacy, leaving his elite guards dead, his prisoners escaped, and his reputation in Brassmoon ruined. When Dellyn finally faced Thaco and was defeated, he expected to be killed and earn a place in the legends of goblins as their racial nemesis until Thaco told him he was not worth the XP to kill.
Complains: "You fought the Goblinslayer? Did you kill him?" Thaco: "No. I destroyed him."
Done in Girl Genius. After Dr. Beetle dies, Baron Wulfenbach tells Dr. Merlot that for his part in the incident, he'll be put in charge of the city of Beetleburg...after Dr. Beetle has been given a hero's funeral with full honors, and the full details of Dr. Beetle's death, including the fact that Dr. Merlot's theatrics were the direct cause of it, have been released to a public that loved and respected Dr. Beetle.
Done in a social way for humor in Eerie Cuties, to set up for its spin-off, Magick Chicks. After the Hellrune Coven have tried to use a gender-bending magical orb for a small plan that turned into a fiasco that left one boy stuck as a girl, they're called in front of the headmistress. Since they're also the "Queen Bees" of their school, they're told protocol would demand they be expelled. However, the headmistress believes that would let them off TOO easily. So she talked with the head of Artemis Academy to get them transfered over there as part of an exchange program, forcing them to start all over without any socal benefits from their soon-to-be-former school. To a young girl who fought a lot of her high-school life to be popular, losing your status and being "socially dead" is worse than a physical death.
Ink City: Trevor pulls this on Mew, with a twist of manipulation: originally, he was poised to take his revenge on anotherMew who had just arrived. He waited until Mew publicly confessed before informing her he wasn't going to seek his pound of flesh; watching her live as an outcast would be far more satisfying.
Chakona Space: Allen Fesler's character, Neal Foster has pulled this off a few times.
In the YouTube Poop "One more Final: I need you(Tube Poop)" Luigi refuses to kill Link despite his pleadings, preferring to let him live with his misery.
Explicitly invoked in the Centurions episode "Cyborg Centurion". Ace McCloud is in a deeply nasty area, and has to fight a local tough to establish his credentials. The woman he's with asks Ace, "Why didn't you kill him?" and Ace tells her "I did worse than that. I humiliated him and let him live. He'll never command respect from these people again."
Optimus Prime refuses to kill Big Bad Megatron, who had just caused the deaths of one of his soldiers minutes before, during the finale of Transformers Animated, telling him, "That would be the easy way out, Megatron. You don't deserve it." Instead he destroys Megatron's weapon and drags him back to Cybertron to face justice in stasis cuffs, humiliated.
One of the most memorable aspects of the Avatar The Last AirbenderGrand Finale is this trope: Aang doesn't kill Phoenix King Ozai, but takes his ability to firebend from him. Knowing Ozai, it would be a Fate Worse than Death, which isn't to say he didn't deserve it. He's also left to rot in a cell (the same cell where he imprisoned Iroh no less) as a powerless wreck while the son he hated becomes the new Firelord.
Azula pulls this on herself during her Villainous Breakdown. She hallucinates her mother, and this follows, completely breaking her world view.
Ursa: I think you're confused. All your life, you've used fear to control people like your friends Mai and Ty Lee. Azula: But what choice do I have?! Trust is for fools! Fear is the only reliable way! Even you fear me. Ursa: No. I love you, Azula. I do.
It could be said that Azula being sent to a mental facility after her Villainous Breakdown could be considered this. She, a massive perfectionist and control freak, is now unable to so much as take care of herself anymore and is completely insane. But it could be a subversion as it's hinted the reason for it is to try and get her back to normal.
Katara does this to the man who killed her mother. After finding out how horrible his life is, she decides to spare him so he can continue to endure it.
In King of the Hill, Peggy confronts Cotton on his deathbed to Call The Old Man Out for being such a horrible, emotionally abusive father to Hank, who only ever wanted his father's love and approval. She takes a hint from one of the page quotes above by saying she hopes he will never die, so that he may live forever in the hell that he has created for himself. Cotton, just to spite her, responds "Do you, now?" and dies immediately thereafter.
In "The Dragons' Graveyard," the darkest episode of Dungeons & Dragons, the kids have finally had it with Venger constantly attacking them and preventing them from getting home. Against Dungeon Master's wishes, they attack Venger, and finally have him at their mercy. Hank could easily kill him, but finally spares him, saying verbatim that "If I did, we'd be no better than you are." But Hank makes it very plain to Venger as they leave, "We've beaten you, and you know it."
Grimian, a member of the Vandals in Hot Wheels Battle Force 5, overthrows Captain Kalus but instead of killing him, spares his life so he may live in shame. When Kalus returns and defeats him, he tells him the exact same thing and promotes him to his second in command so Grimian can live in his shadow. After Grimian sells out the Vandals to the Red Sentients, Kalus and Grimian have a final battle, ending with Kalus' victory. After destroying Grimian's car, he banishes Grimian instead of killing him, once more prefering the traitor live in shame rather than die in battle like a warrior. However, after his next attack, which has the entire planet invaded, Kalus just executes him.
While he doesn't see it as such, Zemerik, under the control of the Alpha-Code, forgiving Krytus is seen at this by Krytus. Krytus had just finally got his revenge on Zemerik for betraying him, but forgiving him, Zemerik also rendered Krytus' revenge meaningless.
In the Justice League episode "War World", the gladiator Draaga fights the despotic ruler Mongul; Draaga defeats him, but refuses to grant him a warrior's death, preferring to let him live in disgrace. (This may or may not have been a mistake on Draaga's part. Mongul does make a return appearance... But what ultimately happens to him could well be considered even worse, depending on your point of view.)
One of the many, many arguments thrown about between pro-death penalty / anti-death penalty groups is the theory that spending the remainder of one's life in prison is a harsher sentence than being executed.
This is practically the argument of philosopher Michel Foucault in his book Discipline and Punish: someone who went into prison and served their sentence, more often than not, will find it far harder to integrate back into normal society, essentially being marked wherever they go.
Invoked some time ago in Italy by some lifer prisoners who requested death penalty to be restored, because they found spending the rest of their lives in prison an excessive punishment.
Turkish Sultan Alp Arslan did this to the captured Byzantine Emperor Romanos IV after crushing his army in the Battle of Manzikert. His own court quickly deposed him, and later had him blinded.
Julius Caesar specialized in this, often showing clemency to defeated rivals especially in Rome's civil wars, which, under the rules of Roman high society, left them permanently beholden to him because they owed him their lives. Cato the Younger actually killed himself to avoid this.
An infamous example happened to Lucio Fulci's The New York Ripper in 1984. BBFC director James Ferman got creative with the punishment he had in store for the film for potentially violating British obscenity laws of the time. He didn't order any print to be destroyed; rather, he ordered all prints within the UK to be returned to Italy.
This is one aspect of the Counting Coup practice among the Great Plains Indians. It sends the message, "I can lay my hands on you and there's not a damn thing you can do to stop me. You are so far below me that you are not even worth killing."