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Vampire Game, the heroine's aunt Ramia may be an Alpha Bitch who mistreats her sons and favors one over the other, however SHE has standards. When a vampire suggests that she kill her adopted son's mother, who is a prostitute, who Ramia strongly dislikes, she responds by saying that even though she doesn't like her, she's still a citizen of this country, and I'm obligated to protect her. She then tells her to beat it. She also cannot stand their uncle's misdeeds.
In the second season of Space Battleship Yamato, the evil emperor-without-an-empire Dessler discovers that the court intrigues of his allies on the White Comet transgress even his moral limits. Particularly when he winds up in their prison cell.
In Black Cat, Train Heartnet, a professional assassin who has killed plenty of people, will NOT kill women or children. Once he was going to kill his target and then he noticed that his intended victim was holding a young child, and he hesitated and couldn't pull the trigger, which led to him getting shot. Considering he reforms later on in the series, this, along with Saya's death at the hands of his partner Creed is probably what caused him to give it up.
In Detective Conan, although the mysterious and beautiful criminal Vermouth has killed many people, she will not kill the protagonist, or his love interest; this probably has to do with the fact that they saved her life a year ago, and Conan is the son of Vermouth's friend Yukiko Kudo. Things get really interesting when Ran sneaks in the trunk of Jodie's car and tries to stop Vermouth; her mook immediately starts shooting, but Vermouth yells at him and tells him to stop shooting. As Ran protects Haibara, (whom Vermouth hates), Vermouth shoots around her, and tries to get her to release Haibara.
Among the first things Legato Bluesummers does in Trigun is wipe out a group of slave traders. While he is an Omnicidal Maniac, he then goes up to their "merchandise" and tells them to make the most of their lives (because they're going to be short if he has any say in it).
This has a lot to do with Legato's undisclosed-in-the-anime past. He was a former Sex Slave, so although he hates humanity in general, he hates slave traders most of all.
In Pokémon, although they're not evil, Jessie and James are Team Rocket agents - kidnapping Pokémon is part of their MO. They do not believe in trainers hurting Pokémon, however, and this is why they (and Meowth) were appalled by Paul's method of training.
"Team Rocket may be rotten cheaters, but we're not in the business of destroying children's dreams!"note "At least, not yet."
This also shows in how they treat their own Pokemon with a great deal of care. They also have been shown to be disgusted by more brutal Pokemon Poachers and trainers and haven't been shown being brutal or overly mean to their captives, unlike some other more evil Team Rocket members shown in the series. (Though the captives's trainers are a "fairer" deal, as once in Advance Generation they almost kill Ash.)
In "The Stun Spore Detour" after Misty helped James and Meowth heal Jessie's paralysis from the Vileplume's fumes, the female team rocket member still wanted to try and capture Ash's pokemon thinking he and his friends would still be weak from trying to recover from their own wounds. James and Meowth refused to help, Meowth even looking physically sickened by Jessie's coldness, and when she got knocked out by her own pokemon, they chastised her for being ungrateful.
Paul himself has several, while it is true that he releases his Pokemon after they're no longer useful to him or failed him. He is at least upfront about his harsh training, compared to the other abusive trainers in the past such as Damian (Charmander's previous trainer). Upfront to Pokemon, that is. While Damian lied to Charmander that he'd come back, he had no problem telling people how he feels about "useless" Pokemon.
Paul was also loudly against the Sunyshore gym's then current policy of just handing out a badge to anyone who came to the door. Jerk or not, Paul definitely doesn't cheat his way to his goal.
Slayers Next. Gaav concentrates all his resources on trying to kill Lina, because he believes his archenemy Hellmaster Fibrizo will use her to destroy him. However when confronting Lina he still gives her the chance to fight back; and when she casts the Ragna Blade and Gaav knows the spell could kill him, he still gives her the chance to attack first and doesn't try to pull any dirty tricks. Ultimately this leads to his demise; although the Ragna Blade doesn't kill him it weakens him enough for Fibrizo to step in and destroy him.
Omnipresent throughout Mobile Suit Gundam. Even many Mooks draw the line at killing women or children, and Ramba Ral dies as a result of such morality. The most obvious use is in the case of Gihren Zabi, an individual so vile that many of his mass-murdering allies find him disturbing. His father, himself a fascist dictator who likely murdered his predecessor in order to gain power, compares the man to Hitler unfavorably. And his sister, who's spent her time establishing her uberbitch credentials, hates him so much that she ends up killing the man for ordering patricide.
Also, in Mobile Suit Zeta Gundam the Titans are a brutal elite force that fights the AEUG and commits lots of atrocities while at it, but many of its members are repulsed when it comes to gassing entire colonies. In fact, the Face-Heel TurnReccoa killed The Dragon for having sent her in a mission that, well, had her gassing a colony.
In Mobile Suit Gundam Wing, OZ leader and Magnificent Bastard Treize Khushrenada was vehemently opposed to the Romefeller Foundation's Mobile Doll System, feeling that they would make humans unnecessary for battle. As a result, he resigned as Chairman of Romefeller, and OZ soldiers loyal to Treize split off to form the Treize Faction.
In episode 13, two of Noin's former students are pretty ruthless when they attack remnant forces of the Alliance, and refuse to accept surrenders even when they're offered. When Zechs joins with them in a later attack, he orders the Alliance forces to surrender, and is appalled that the two OZ troops are still attacking surrendering troops. One of them is killed by the Alliance who feels Zechs betrayed his word in a last ditch attack. The other one starts attacking Zechs partly out of vengeance for his friend, and partly because he felt Zechs was too lenient on the enemy forces. Zechs ends up destroying the other OZ trooper's mobile suit as a result.
In Mobile Suit Gundam SEED, the people inside Jachin Due are shocked when they hear Patrick Zala give the order to aim GENESIS at the Earth. One aide, Ray Yuuki, tells him that it would kill half of Earth's population and destroy the surface; Patrick shoots him. When another aide warns him that the other ZAFT soldiers are in the line of fire, Patrick tells them it's for their victory and that the Natruals must be eradicated. Ray uses the last of his life to shoot Patrick.
Marida Cruz from Gundam Unicorn is a Tyke Bomb and former Child Soldier, but draws the line at killing non-combatants. During the first episode, she revives a group of workers she had knocked out during her pursuit of Princess Mineva, and later saves the life of one her captors after a hole is blown in the side of the Nahel Argama. She's even shown to be distraught upon seeing that her attack on Industrial 7 has resulted in civilian casualties.
Bleach: A case can be made for Mayuri Kurotsuchi. When he's first introduced, he's a Mad Scientist with a horrifically sadistic personality, who delights in torturing his victims for research - something to which Uryu Ishida's grandfather fell victim. However, he remains loyal to Soul Society after hearing of Aizen's betrayal, and never considered defecting to his side. While he would probably have killed Szayel anyway, he became shocked when his daughter Nemu was abducted and practically raped by him to revive himself. (And this is the Artificial Human daughter whom he mistreats to a big degree.) Yeah, Mayuri is a weird case.
Though he isn't loyal to the SS on a moral basis, they are just in a better position to allow his research loving agenda than Aizen. When he first heard about Aizen's betrayal he didn't really care or indicate any anger about it.
Ulquiorra calls Nnoitra "disgusting" for telling him that Ulquiorra should apply molest or rape a captive Orihime; in scanlations, Ulquiorra's response ranges from "how vulgar" to "you degenerate scum." Unfortunately, Nnoitra is more than happy to try taking his own advice when Ulquiorra isn't around.
Grimmjow doesn't care about anybody and doesn't even mourn for his own subordinates after they die in battle, but even he seems pissed at Loly and Menoly's No-Holds-Barred Beatdown on Orihime. True, after he performed one awesome mix of Big Damn Villians and Kick the Son of a Bitch, he demanded a favour off her, but he still told her to heal her face and took the time to find a cloth so the handcuffs he put on her wouldn't damage her wrists.
In the OAV Riding Bean, Bean Bandit is a professional wheelman with a soft spot for kids. In Gunsmith Cats, nothing's changed. In one volume, Rally sees Bean, after delivering a package of drugs, stuff a drug dealer down a manhole for trying to sell drugs to kids. Rally challenges him to a race on the condition that if she wins, he'll give up doing drug-related jobs period. They finish in a draw, but evidently the Bean Bandit was so eager to give up dope-running that he concedes defeat.
Priscilla in Claymore. While she's ready to kill and eat men, women and boys, she doesn't kill girls. Because helpless girls remind her of her childhood trauma: when she was a child, she watched as her father was possessed by a monster and ate the guts of her mother and siblings right before her eyes, and while he chowed down on her sister, she snuck up behind him and cut off his head with a knife. No wonder she has issues.
Comedic Sociopathy is the norm in Ranma ˝. Yet even Nabiki, heartless enough to sell photos of Ranma's female side to hornball men as a supplement to her pocket money, and who went so far as to sorta whore him out during her stint as his fiancée, is disgusted when Genma reveals he regularly stole food from the juvenile Ranma. Akane Tendo, who has no qualms about beating her fiancé senseless when they fight, is horrified at the extents Shampoo is willing to go to in order to try and drive away her Stalker with a Crush, Mousse. And Genma, perhaps the one of the purest Jerkasses in the series, is disgusted by the antics of Panty Thief and Lovable Sex Maniac Happosai.
Phoenix King Saffron, a spoiled brat who mistreats his subjects and thinks nothing of kidnapping, killing, or blackmailing, tries to incinerate Ranma with one of his fireballs. Ranma tosses Akane's doll-like body note not really, it was just her clothes as a decoy, since it absorbs heat. Saffron is aghast and declares Ranma to be a wretched coward.
Ranma himself, who has been known to exploit his feminine side for free food, belittle his fiancée for her lack of feminine skills, and prance around nude in his girl form, using his lack of feminine modesty to distract opponents... has stated that he believes that the lowest of the low are men who come home drunk and beat their wives. And he himself is sometimes put off by how badly Shampoo treats Mousse.
In Yu-Gi-Oh!, when Pegasus notices Bandit Keith pulling cards from his wristband during his duel with Jounouchi, he waits for Jounouchi to win, then calls Keith out both on his cheating during the duel, and stealing Jounouchi's entry card to try and get him disqualified. Pegasus then has his security guards haul Keith away and congratulates Jounouchi on winning in spite of Keith's dirty tactics.
Indeed. Pegasus never makes any secret of the fact that he can read minds, nor (unlike Keiths's cheating) is it actually against the rules
In the second season, Marik decides to cheat by using Rishid, who is posing as him, to use the (fake) Millennium Rod to release Bakura's good half, who is confused and wincing in pain from the fake injury Marik gave him, since Yugi wouldn't be likely to attack Bakura in that state. Yami Bakura can't let this happen since he needs Good Bakura's body, so he betrays Marik and gets defeated.
That's more like Pragmatic Villainy. Yami Bakura didn't do it because he had standards or because he cared about Bakura, but because if Bakura was killed, he'd cease to exist.
In the third season, Noah intervenes to stop Ooka from cheating with his duel with Jounouchi, irritated since he wants his cronies to best Seto and his friends fair and square. If it weren't for Jounouchi convincing him to let the duel continue, Noah was set to stop the duel since by all accounts Jounouchi would have won by then if Ooka hadn't cheated. (Unfortunately, Noah later proves little better than Ooka, and unlike Pegasus, there are very few mitigating factors to excuse such behavior.)
And in season four, Raphael refuses to allow any of his monsters to remain in the graveyard, even sacrificing his own life points to return them. This is sympathetically explained because he's an orphan who horribly lost his whole family.
In Yu-Gi-Oh! 5Ds, Rex Godwin had nothing but disdain for Takasu, a prison warden who abused his power, framed the inmates for rules violations (among other abuses), cheated as a duelist, and was generally a disgusting person, and eventually fired him.
In Yu Gi Oh Zexal, Vector is more evil by far then the other six Barian Emperors, and none of them like him very much. (Alit, especially, seems to have nothing but contempt for him, and Durbe actually had to hold an angry Mizael back to prevent him from attacking Vector after he insulted the defeated Alit and Gilag.) In fact, Vector appears to be the only one who has actually been witnessed doing anything that could be truly considered "evil", other than fighting the good guys. (Gilag has Brainwashed a few people, but such victims don't seem to be permanently harmed by it.)
The German anti-robot KKK-expy in Pluto is nonetheless appalled by the murder of robot children, even though they don't look remotely human (or even cuddly).
The younger Toguro brother in YuYu Hakusho, while having sold his soul and became a contract killer, obeys a strict code of honor, almost never killing people unless it's specifically part of his current job, and displaying great dislike for those who commit dishonorable acts. When the older Toguro brother plays mind games during his fight with Kuwabara, the younger Toguro demands that his brother stop, and is pretty visibly pissed off. Also, when his same brother attempts to interrupt his one-on-one fight with Yusuke, little brother finally gets fed up with his elder and nearly annihilates him with a single punch. Toguro also killed the entire tournament committee because they tried to tip the scales of the Urameshi/Masho round in Team Masho's favor using their executive power. Seriously, do not act dishonorably in front of the younger Toguro.
Granted, elder Toguro was practically spitting on Genkai's name, who younger Toguro loved and killed the night before. It's possible he was still very bitter about the whole incident.
During the Urameshi/Masho round, Kurama passed out while standing after the second consecutive victory. Due to the aforementioned committee, he was forced to fight the third round while unconcious against Bakken. it went about as well as you think it would. The fight was in such bad taste, even the sadistic announcer tried to stop the fight numerous times just because Kurama wasn't conscious to "enjoy" the beating, too.
In Black Lagoon, you can throw a stone anywhere in Roanapur and you'll find that whoever it hits or lands near will have more standards than Chaka. Even the Neo-Nazis had more class than him.
Revy: Wow, this is surprising. You shot your own subordinates. Despicable to the end. (setting aside the fact that she herself has killed non-combatants on more than one occasion. Well, non-combatants that she had no attachment to.)
In Transformers Armada, when Starscream defects to the Autobots, Hot Shot points out that Sideways has already betrayed them. Starscream gets angry that they would compare him to that bastard.
In One Piece, Dragon-in-Chief Rob Lucci is an Arrogant Kung-Fu Guy, Psycho for Hire whose idea of a hostage rescue is "massacre everyone so they don't have to live with the shame." However, he is visibly disgusted when his far weaker boss Spandam beats Nico Robin while she is tied up, helpless, and unable to use her powers to fight back.
He also sneers at him when asked about why he didn't do anything about Chimney following them and finding the way to the gate, later telling Luffy how to get there as well. Whether that's because he dislikes Spandam or he simply doesn't wish to kill children is up to your interpretation, though.
While it makes sense that Lucci wouldn't be interested in killing a defenseless child, he refrained from stopping Chimney because he wanted Luffy to find him so they could fight. It's obvious that he dislikes Spandam either way, though.
Absalom is a huge pervert who does not shy from sexuality assault, and likes weaker women who can't fight back, and stabs Sanji in the back surfing fight, seems genuinely concerned with Perona's abuse of Bearsy.
Eustace Kidd is a sociopath with a HUGE body count on his head, killing people For the Evulz or for being weaker than him(although he says he kills people who look down on him or insult him). But slavery is something he would never involve himself in. Kidd's reasoning is At Least I Admit It: sure, he's done his share of killing and pillaging—but taking into account that he's a pirate, it's to be expected. The Marines and World Government, on the other hand, espouse "Justice" while allowing slave rings to operate unchecked, making them hypocrites on top of being evil.
Chief Jailer Shiryuu's bloody rampages across Impel Down have made Magellan, Impel Down's chief warden, very displeased, particularly as he had no damn reason for killing off prisoners, and he was forced to imprison him in Level Six as he was far too dangerous to be ignored. Given the fact that Impel Down is likely the worst prison in fiction where all the jailers are cruel sadists, Shiryuu's treatment of the inmates must have been horrid beyond belief.
Blackbeard is quickly becoming the Big Bad of One Piece, having killed a crewmate for a Devil Fruit, handing in his former commander Ace and thus causing the Whitebeard War that lead to the end of the Great Age of Piracy and the beginning of the lawless hell that is the New Age, recruited crewmembers by having the residents of The Alcatraz rip each other to shreds and taking whoever was left, but even he listened to Coby's speech for them to stop fighting. Blackbeard would also never make funny about other people's dreams and take them serious.
Helmeppo has no morals about lying to prisoners, bullying townspeople, or throwing kids over the fence. Killing kids is another story and he's genuinely shocked when his father kills off an officer for disobeying a kid-slaying order. Probably why he gets a genuine Heel-Face Turn when he is pressganged into the Marines.
While Luffy is far from evil, he can be pretty chaotic as a pirate and does what he wants. During the Impel Down arc, he was willing to ally with several potentially dangerous criminals and former enemies in his quest to save Ace. However, he draws the line at freeing Crocodile, as even Luffy can't overlook what he's done. He's freed anyway.
Arlong is a racist who crossed the Moral Event Horizon by killing Nami's stepmother, and treated Nami like crap for years. But he treats his own men like family and called Luffy a coward when the latter used his True Companions as a shield. It gets an echo during the Fishman Island arc, when one of the leaders of the Fishmen Pirates decides to use one of their own True Companions as a shield for one of the attacks of the Straw Hat Pirates and they were appalled by it. Also in his backstory, Arlong was appalled by Jinbe's brutality towards humans. Ironically, he lost those standards as time passed while Jinbe softened and is now one of the Straw Hats' allies.
It was surprising when it was revealed that even Admiral Akainu had standards. He had clashed with Aokiji over who would become the next Fleet Admiral with the latter heavily opposing his ideals and promotion. Their conflict eventually led to them having a fight to the death to see who would become the Fleet Admiral. In the end, Akainu won but he decided to spare Aokiji. It was lampshaded that even Akainu couldn't face his previous ally without some sympathy.
When Sanji and Franky witness an example of You Have Failed Me from Rob Lucci, their reactions are this;
Sanji:These are the agents of justice...? Franky: They're more evil than we are.
The G-5 Marines are sick bastards who like to torture captured pirates just for fun. But when they encounter Trafalgar Law, who became one of the Seven Warlords of the Sea after sending the hearts of 100 pirates to the World Government (Given Law's power, there's no guaranteethat they're even dead), they got scared and called him "insane" and "a creep".
A better example is given at the end of that arc, after their Enemy Mine with the Straw Hats. They badmouth the Straw Hats as if they were the usual variety of pirates because if they don't, they'll admire them.
Later, Smoker and Tashigi are discussing cases of children being kidnapped in recent years. Tashigi thinks that someone in G-5 was involved in those cases, and tried to cover up for them by sending fake reports to the headquarters. When Smoker pointed out that this is what Tashigi meant, the G-5 Marines got pissed as soon as they heard that, saying that even though they are army rejects, they still have their pride as Marines.
Perhaps the biggest One Piece example of this trope (to this point) is the World Government's attitude toward WMD. Apparently, the same organization that invented the Buster Call and is responsible for multiple forms of genocide and other atrocities is somehow appalled at the usage of chemical warfare, such that they've deemed it illegal and attempted to imprison one of the leading researchers on it (and of it, considering his Devil Fruit), albeit after the latter created an "accident" at a research facility.
Trafalgar Law has a pretty nasty reputation as a pirate, but when Caesar Clown told him that he had drugged the children he kidnapped in order to prevent them from escaping, even he was disgusted. There's also the respect that he shows to Luffy, allegedly due to him being a Worthy Opponent.
The main reason Don Krieg stopped at the Baratie restaurant was not just so he could eat because he was starving, but because his crew was starving as well and he couldn't just stand by and let them starve. That and he wanted a new ship because the old one was falling apart. Not all pirates are that bad.
However, he most likely did that so he wouldn't lose his manpower at hand.
In the twelfth movie, Akainu found Z to be a bit extreme with his methods. Admiral (Ripper) Akainu, who as mentioned above (using his real name, Sakazuki) would sacrifice a thousand innocent people to potentially kill one "criminal" (An eight year-old girl whose only "crime" was to be a scholar), and has done so before, thought he was extreme.
Which makes sense, considering that Z's plan involved turning the entire Grand Line into a fiery wasteland. While it would undoubtedly kill all pirates, the sheer amount of property damage and civilian casualties, plus the thousands of marines that would die in the crossfire, was too much, even for Akainu.
Anti-Hero Fukunaga of Liar Game, despite perfectly willing to deceive and lie to others to benefit herself/himself, snapped on a teammate during the Musical Chair Game when he suggested that Nao should be the one to be degraded to the Gaya group (where she would have no chance in advancing to the next round), declaring that they shouldn't put that kind of pressure on Nao who isn't even the room at the moment. So naturally Akagi lampshades this.
Oddly enough, Zolf J. Kimbley comes off as this in Fullmetal Alchemist. He's perfectly willing to let Pride kill Ed so long as he does it in a sufficiently dignified and awesome way. Kimbley comes to Ed's aid simply because he can't stand the idea of someone supposedly innately superior trying to save themselves by clinging desperately to an inferior's body and verbally bitch-smacks Pride before leaving the planet for good. Kimbley has a strict code by which he lives and judges others. This code has nothing to do with morality, but rather being true to one's convictions. To him, the lowest of the low are hypocrites.
In G-Spot Express, Katsu beats up a gang of rapists when he sees them attacking Yumi (whom he just happened to have molested in the past himself). However, he also allows Ginji's crew to rape Sayaka after she arrests a friend of theirs.
In Umineko no Naku Koro ni, the sadistic Beatrice takes young Maria Ushiromiyaunder her wing, because she's utterly disgusted by her mother's Rosa's abuse of her. This action is the downplayed variant of the trope, however, not stopping her from killing every other member of Maria's family in horrible, horrible ways - including the people in it who are actually nice to her... and more strangely, she also allows Maria to go Calling the Old Man Out to fatal levels, while commenting on how Rosa and Maria's relationship is sad and poisoned. Beatrice also really dislikes a witch that is worse than she is (Eva-Beatrice), and in the games she tells that to her very face.
D.Gray-Man: Wisely used an Exposition Beam to show another character Kanda's childhood memories. Allen is sickened and profoundly pissed off, and Kanda is in a Heroic BSOD state. Kanda. Even the local villainous Creepy Child Road, who delights in Mind Raping people, seems to be upset by it.
Towards the end of the Live-Action Adaptation of Death Note, Misa Amane, previously an amoral mass-murderer at worst and a Psychopathic Manchild at best, is genuinely shocked and starts to cry when Light writes his own father's name into the Death Note. Which is justified, since it comes from her being an orphan with serious issues about it and having that side of her being given much more attention than in other DN media.
In the manga and anime, during Light's first meeting with Ryuk, the latter is stunned by how many names Light has written into the Death Note in just five days. Protip: if your murderous rampage gives a god of death pause, you might want to scale back a little. Then again, this could also be understood as him being impressed, since he also tells Light that most gods of death are shirking their duties and that Light himself would make a pretty epic Shinigami. Double-subversion comes during the clip showing L's funeral. A montage of Light's killing spree is briefly interspersed with a single clip that strongly implies Ryuk was very strongly considering writing Light's name in his own Note. An interpretation being that even Ryuk, who set all of this in motion For the Lulz, is surprised by the absolute craziness Light generates, another is that he may have been legitimately scared of Light killing him with a Gambit Roulette just like he did with Rem.
There's also Higuchi. His Evil Laugh scares Shinigami.
Despite all Light will do for his plans to succeed, he can't bring himself to write his sister's name in the Death Note. Though, that might have been partly motivated by how his plans would turn out if he did kill her.
Light is initially dismayed when Mikami's killing spree extends to even relatively innocent people guilty of such minor acts ad being lazy, but later thinks to himself only that it's "too early to be making statements like that," suggesting he may agree. Explicit in the manga when he actually toys with this very idea early on in the story.
Rem has no qualms with Misa murdering innocent people, as well as murder being committed for her sake, but is repulsed by Higuchi's greedy and obsessive nature.
Could be argued of Stein to Medusa in Soul Eater, given their fight was on the basis of pitching two violent anarchists against one another to see whathappened. Stein is clearly attracted to Medusa's point of view (amongst other things) and claims that only fear of a higher authority (i.e Lord Death) holds him back. But when Medusa claims she is the mother of the child she's been experimenting on - Crona - and that she would gladly sacrifice 'it' if necessary, Stein is visibly angered by her. However, later chapers make an attempt to make Stein appear more humane and not simply the 'hedonistic sadist' Spirit pegs him as during the fight, so the 'evil' is debateable.
Arache was dubbed a 'heretic' by her own kind when she killed a witch in order to create the first Weapon. As the witches are largely presented as Always Chaotic Evil, this probably counts.
Kiyotsugu Gowa from Gasaraki is a Mad Scientist, but he's appalled when he finds out that his own sister Misuzu is a kai (a person able to synchronize with the mecha of the series) and refuses to tell this to his brother Kazukiyo out of fear of what he'll do to her. He also refuses to use an untested and fatal Psycho Serum on test pilots, so another Mad Scientist does it instead.
In Holyland, most gangsters don't respect Combat by Champion and gang up on the victor if he's not the one on their side. Thus, it stands out when the gangsters gathered to watch Yuu fight Katou refused to gang up on the former and when the latter was beaten, some of them, including Tsuchiya, did not want to lynch the victor. This foreshadows Tsuchiya's Heel-Face Turn.
Later on, even Ryuu, the more insane of King's two henchmen, is creeped out by Katou.
In Naruto, more than one villain is repulsed by another's actions. In example, when Kabuto reveals the Edo Tensei technique that lets him raise a zombie army of powerful ninja while also desecrating their corpses, we see that Tobi is repulsed by said strategies and is blackmailed into going along, with the source of blackmail later revealed: the real Madara Uchiha, bringing into question who the repulsed one was.
Earlier on, Zabuza Momochi expresses his disgust with Gato for double crossing him (and desecrating Haku's corpse), and is extremely pissed off because Kabuto brought him and several others back from the dead to use as mindless drones.
Zabuza: This is bullshit, I don't want to fight for someone who would stoop this low.
When Kabuto later revives the real Madara Uchiha as an Edo zombie, the nine-tailed fox sealed inside of Naruto offers to give Naruto some of his power (without trying to take over his body). Why? Because he REALLY hates Madara. Anyone halfway decent hates Uchiha Madara, even Kurama; he's that much of a dick.
Obito is getting tired of Madara's rampant cruelty and even calls him out on being a 'kid' for testing the Ten-Tails power even though the entire plan is supposedly Infinite Tsukuyomi.
The main villain, Dr. Eggman, from Sonic X who once tried to blow up a city of completely innocent people, can't stand torturing victims as shown when he witnesses Black Narcissus torturing Chris and Cosmo and he says, "I'm not above evil myself but torturing people is just plain wrong."
He also in one episode alerts his arch-nemesis, Sonic, that the Metarex are planning to kill him and his friends stating that "if anyone is to get revenge on that hedgehog it's going to be me! And through less brutal means!"
When Sonic is apparently stuck on earth while his friends are in their world, Tails, an 8 year old, takes on Eggman's new space carrier in his plane. Eggman orders his Hench-robots to fire a homing missile which homes in on the plane. When the missile is near to hitting Eggman says to call it back (he only sent it towards the plane to scare Tails) however is told that there is no "call back" button. Eggman is horrified at the thought that he has killed a child. Tails, however, is saved in the end.
"I'm going to have to live with the thought of killing Tails forever!".
Eggman seems to have a soft spot for characters such as Chris or Tails perhaps because they're the smart, logically inclined inventors of the group and thus maybe they remind him of himself. When Tails has to kill Cosmo in the third season finale, Eggman is the one who talks him through it and reassures him that he knows how difficult it is, but it's this or the end of the universe. While he accepts that it's necessary, he doesn't celebrate killing a child, nor does he celebrate the fact that one of his arch-nemesis's friends is the one who has to do it.
As shown in the season one finale, where his robot is going insane and beating poor Sonic to death. Chris (who was Eggman's prisoner at the time) is crying for him to stop. Eggman tries to get his robot to stop.
In the light novel of A Certain Magical Index, Accelerator quotes this quite often when fighting other evil people, then goes to show them "what being a true villain is all about" usually ending with a swift death.
Ironic because Accelerator himself has moments of this trope, especially when Last Order is around.
Shizuri Mugino, one of the most psychotic characters in the franchise, is sickened and horrified by cannibalism.
Alucard may be an Ax-CrazyCombat Sadomasochist, but he knows when someone goes to far. One of the reasons he serves Hellsing is because he hates the vampires of the modern era not only for being far weaker than he is but also for abusing what little power they do have. Specifically by turning people into gouls, and Alucard is above that. And the Major starting a war on England just because he liked war... even Alucard thought he was a lunatic! Sure he killed a bunch of human police officers when they stormed into the hotel he was staying in, but at least he did it for an actual reason! Plus, due to his Undying Loyalty to the Hellsing Organization, he has a strong distaste for traitors. Lookin' at you, Walter.
And becoming a monster for the sake of defeating him? He... doesn't approve of that either. Anderson finds this out the hard way.
Enishi from Rurouni Kenshin slaughtered a family - babies and young children included - who nursed him back to health, just because he was sickened at the fact that they were living happily while his older sister Tomoe was dead, but it's been implied that he doesn't kill young women. Not that Enishi might not want to kill them, but because he psychologically can't kill young women because of the nature of Tomoe's death, who was around 17/18 when Kenshin accidentally killed her in front of a 10-year-old Enishi. This was why Kaoru (who is around the age Tomoe was when she died) was spared in Enishi's plan for revenge against Kenshin, and instead of being downright murdered, Enishi went through the trouble of hiring a master puppet maker to craft an extremely elaborate doll in Kaoru's exact likeliness.
Can also be seen in Gein, who is extremely disliked by his own companions.
Akira Hongo, the "God Fist" of the antagonist YAMI group, proves to be an interesting case of this trope. At one point, while he's confronting Kenichi and Miu about the death of his disciple Shou Kanou in the earlier D of D Tournament arc, Ryozanpakou masters Shigure and Apachai attack him. However, he effortlessly puts them off without actually fighting back, because Apachai is still injured from his earlier fight with his rival Agaard (a fellow YAMI member) and because Shigure is a woman.
Speaking of Kanou, a flashback near the end of the D of D arc reveals that, for all his cool-mannered exterior, Hongo really did care about his disciple. In the present day, Hongo was greatly displeased upon first learning that Kanou was dead.
Much later, Hongo did not take it well when other fellow YAMI member Silcardo Junazard tricked him into almost killing Kenichi while he (Akira) was fighting in an unconscious state in order to fulfill his bigger objective of kidnapping Miu. He wound up in an Enemy Mine alliance with Ryozanpakou because of it.
Apparently, the One Shadow Nine Fists group leading Yami has a good degree of standards, as nearly all of them care about their respective disciples in their own way and are at least willing to submit to the unspoken rule between them and Ryozanpaku that master-class fighters should not interfere in their disciples' fights nor interfere in a match between two other master-class warriors. The sole exception among the Nine Fists is Silcardo Junazard, who has broken both rules, showing himself to be very willing to kill his own disciples if they don't meet his standards, and crossed the Moral Event Horizonby his aforementioned manipulation of Hongo to nearly kill Kenichi so he himself could take advantage of Miu's chaotic mental state and kidnap her to brainwash her.
In fact, Junazard's misconduct is so severe that we get to see just how the One Shadow Nine Fists group has standards despite being the series' antagonists who advocate the killing-fist aspect of martial arts: Hongo seeks audience with the One Shadow prior to undergoing the above-mentioned Enemy Mine, presumably to get permission to fight and kill Junazard, and the One Shadow himself also gets involved in Miu's rescue, albeit going there incognito.
Isshinsai Ogata, another member of the One Shadow Nine Fists, won't hold back against opponents who step up to challenge him, and won't hesitate to kill you if you fight him with the determination of a martial artist. But as a flashback reveals, he was not happy to discover that he'd unknowingly killed an unborn child when a pregnant fighter stepped up to challenge him. He actually calls that discovery an unfortunate tragedy when it's revealed in the present day.
Panty & Stocking with Garterbelt features the Demon Sisters Scanty and Kneesocks who are pretty determined to take down the human race, but are much more polite and rule-abiding compared to the Jerkass angel protagonists. Perhaps the crowning moment is when Scanty expresses a great disgust when Panty and Stocking are perfectly willing to let Brief die at the Demon Sisters' hands, much less not bother to say his real name.
Likewise, on the angel's side, Panty has almost no moral standards whatsoever, and yet as foulmouthed as she is, she can't stand hearing the word "moist".
The Emperor from Code Geass is a man who allows his people to brutalize, slaughter and abuse anyone in capture areas, simply because they aren't Britannian. He's NOT a nice man and most of the world hates him for very good reasons. That said, he will not stand for lying. He watched his family murder each other in power grabs with lies and absolutely despises anyone who plays a role. As a result, when he found out that his brother had lied to him about killing his wife and Lelouch's mother Marianne, he stole his code and let him die for the action when he had the chance in R2. This does make him a bit of a hypocrite, as Lelouch points out. He put on his own mask as Emperor to hide his true goal of making a world without lies.
Cornelia is a Lady of War, and had her share of war crimes against enemy's population. But if your plan involves nuking your own population, she'll never side with you. Notice that Cornelia hasn't done anything evil since… at least the declaration at the school festival.
Kanon was shocked when Schneizel reveals he has no intention of rescuing his own half-sister Nunnally, since he was using her as a bait to kill Lelouch.
And Schneizel himself is shocked when Euphie is killing innocent Japanese left and right. Although in this case, she was inadvertently Geassed, not intentionally being evil.
A comedic example in the sound dramas of Mai-HiME. Nagi may be a Manipulative Bastard who is working for the evil Obsidian Lord, but he reminds the viewers not to drink before they're 20, unlike Mai, Natsuki, Mikoto, Nao, Chie and Aoi.
In Rosario + Vampire, Kahlua actually begged Gyokuro to reconsider when the latter put a hit on Kokoa.
From Jormungand, Koko Hekmatyar may be a weapons dealer not above making a profit off of war and crime, but you do not harm her subordinates or children in her presence, despite of the fact that she has contributed to the deaths of myriads of people with some children inevitably among them (but hey, since they were not in her presence it's okay right?). And don't even think of paying her in drugs. (Or credit).
In Ah! My Goddess, Marller captures Urd and splits her demon and goddess halves and transfers the demon half into an artificial body. One of the first things Demon Urd does is seal Urd's younger sister Skuld in a magic mirror. Marller thinks this was a little harsh.
Koro-sensei from Assassination Classroom has promised that he will destroy the world in one year's time unless he can be defeated, and yet when one of his students endangers the life of a classmate, he flies into a berserker rage and threatens to kill the boy's family if he ever tries something like that again.
In Attack on Titan, even the paranoid, vicious commander of the Military Police Brigade who was eagerly trying to have Eren executed a few moments ago is stunned at how far Levi goes in his No-Holds-Barred Beatdown.
In Fairy Tail, Despite everything Alpha Bitch Minerva has done at this point even she was frightened to see her Guild Members turned into mere paper by Kyouka of Tartaros, but considering her possible survival and boost in power this might be nothing. Still she also had decided not to just kill Erza when she was in her child form but Minerva replied she was just keeping her alive for her own pride.