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The Hutts in Legacy undergo this after Vul Isen callously slaughters refugees fleeing the genocide of Dac (which incidentally, he carried out). The Hutts might be corrupt, but killing innocent refugees/potential customers is apparently the line they cannot tolerate. Given that the nephew of a high ranking Hutt died for sheltering them, revenge is partially responsible.
This trope explains it all, and made life difficult for the Marvel UniverseNazi villain Red Skull, as the other villains he has teamed with, notably Magneto, have ultimately attempted to kill him. At one point he even left himBuried Alive. Given that Magneto is Jewish (or possibly Roma, depending on which sources you believe) and a Holocaust survivor (in all sources), though, this isn't entirely unexpected...
Still, The Joker is the incarnation of Depending on the Writer, and that was one of the tamer versions, based on the 1940's incarnation who was giggling and flamboyant, but not psychotic at all. Someotherversions probably wouldn't have given a damn, if they'd even partner with anyone else at all.
Also, The Joker does go mano a mano with the Red Skull, though "it ends in a draw": In their fight inside a bomber, the releases on the nuke they are fighting on are released. This causes the bomber's doors to open and dump Skull, Joker and the nuke over the ocean... where the next two pages show a mushroom cloud. Though, they're using the "Golden Age" Joker, where he would have these scruples in World War II.
The Red Skull is a monster even by Nazi standards, and that's the whole point of him (according to the backstory account of Hitler more or less taking him on as a protege on what amounts to a bet that he could make him into the ultimate Nazi.) How monstrous the Skull became is illustrated by what he ultimately did to his mentor: Imprisoned in an inescapable, formless, empty void. By pure trickery. (The fact Hitler wasn't nearly as good a strategist as he thought he was, in real life or comics, probably helped.) Though Doom had no problem giving Red Skull one of his time machines, though that's probably because he got something out of it. The two of them do little more than very rare business encounters. And they've fought on the Moon.
Even Red Skull has his limits. Most notably, when he discovered what Viper did, he booted her off. Viper was blowing his money and resources on mindless terror campaigns; Red Skull is a horrible excuse for a human being, but he's a pragmatic horrible excuse for a human being, and he will not stand for people wasting his time and capital with no gain. Skull wants to rule a world shaped in his own twisted image; Viper is a nihilist who just wants to watch the world burn.
The relatively minor villain Flag Smasher (who attempted to destroy all governments on principle and was a particular foe of Captain America) went directly to Captain America for help when he learned he was being bankrolled by the Red Skull.
Probably the only exception to this is Norman Osborn, who not only tried to help Skull with his plan to gain control of Captain America's body, but bankrolled this endeavour and hoped to team up with the Skull as his own personal Captain America for the Dark Avengers. It makes sense, in retrospect, given this was Norman during his Dark Reign days, where he was very much an expy of Lex Luthor, along with the fact that Norman is a psychotic bigot himself.
Even Carnage, a guy who thought that letting Nazis run rampant would be "fun", decided that letting the Red Skull run rampant is NOT in his best interests.
The Jokerhimself has run into problems thanks to this trope. Whenever a new Society of Super Villains comes together, The Joker is often excluded. Partly because he is not much of a team player and considered far too "unprofessional", and partly because all the other villains are flat fucking terrified of him. Summed up best by this quote from Underworld Unleashed:
The Trickster: Good going, Neron. Pick a guy no one wants to be in the room with. When villains want to scare each other, they tell Joker stories.
On the other hand, Lex Luthor generally makes it a point to invite the Joker to his super-villain team-ups. Granted, he does this for the pragmatic reason that as uncontrollable as the Joker is, it's still better to have him going hog-wild on the heroes than on your super-villain team-up because he thinks you snubbed him. The wrap-up of Infinite Crisis makes this a plot point.
The Joker himself demonstrated this during the Emperor Joker storyline in the Superman series. Given ultimate power, Joker kills Batman in horrific ways after resurrecting him every night, kills everyone associated closely with Batman (Robin, Nightwing, Huntress), eatsall the billion-plus people in China, plans on destroying the entire universe... but when a twisted Jimmy Olsen offers to help the boss by killing Superman (at the time turned into a regular dog), Joker is not pleased.
Joker again shows this with the most literal meaning of "standards" in a Batman/Spider-Man team-up when he teamed with Carnage. The two worked fine until it was time to actually kill their intended targets. Joker wanted to do things in his usual "artistic"/"funny" way and was disgusted at Carnage's plan to just brutally eviscerate them.
Some people consider the Joker's murder of Sarah Essen-Gordon, Commissioner Gordon's wife, in Batman: No Man's Land this. After he shoots her, he walks away from the scene frowning, without a single word. As those other tropers have said, if the Joker himself doesn't think something is funny, it's seriously wrong.
Which is why seeing the Joker stop laughing in his cell at Arkham was one of the creepiest harbingers of the ascendancy of Anton Arcane and his fellow escapees from Hell in Swamp Thing.
In the first crossover between Spider-Man and Batman, the Joker's utterly disgusted with Carnage's idea of killing people. That it, as quickly, messily and painful as possible. Joker doesn't see the creativity of it all and it really cheeses off Carnage, who, until that point, looked up to the clown.
As far as treason is concerned, in a Justice League of America story, Two-Face found out he was potentially involved with the Qwardians for what would have been a plan to take over Earth. When his famous coin "came up clean" (whole/pure side up) he went to the Justice League: since Batman was out of Gotham, he talked to Green Lantern first. It was a shocker to The Flash when he found Two-Face on the Satellite, and it took one of Hal's energy bubbles around Barry to get the Speedster to listen.
Lobo. For all of the Omnicidal Maniac that he may be (just remember what he did to his homeworld), he will ALWAYS stick to his word. ALWAYS. However, Lobo often only keeps the letter of his word, not the spirit, doing exactly what he promised and nothing more... and God help you if you harm his beloved space dolphins.
He was, however, kicked out of Hell and granted immortality so he wouldn't come back. For obvious reasons, Heaven didn't want him either.
In the last chapter of The Monster Society Of Evil, as Mister Mind is being tried, his lawyer, who he knows to be a slick Amoral Attorney, hears of Mister Mind's crimes and tells Mister Mind he hopes he gets the electric chair.
The Mad Thinker, an enemy of the Fantastic Four, showed that there was a line he would not cross in a storyline where he formed a partnership with the Wizard (another enemy of the Fantastic Four) in a scheme that involved kidnapping Reed and Sue Storm's young son Franklin. When the Wizard revealed that the plan would more than likely result in Franklin's death, the Mad Thinker objected to it. Because the Wizard refused to abort the plan, the Thinker dissolved the partnership and contacted the Thing, Franklin's godfather, who aided him in defeating the Wizard.
Arkham Asylum: Living Hell has the Joker talking down to a scam-artist corporate executive who got himself judged "Not guilty by reason of insanity." Granted, he's usually crazily giggling and "playing" with cultural values, and bashing executives sounds right up his alley... except he and the plot are completely serious about this. As far as can be told, the issue here is that Warren White is just an asshole. More specifically he says "I've killed people, but I didn't steal their kid's college funds."
Hilariously, the Joker isn't the only one who does this in the story. Everyone the scam artist meets in Arkham calls him the "worst man I've ever met." The asylum director, Humpty Dumpty, the Joker, and demons from hell. And Humpty is Warren's friend.
Oddly enough, White doesn't suffer from this after he truly goes insane and ends up looking like a sharkman after getting locked in Mr. Freeze's cell. The other villains love him and are happy to take advantage of the services he offers unaware that he made a Deal with the Devil that will let him torture them in Hell after they all eventually die.
Batman villain Firefly, a professional arsonist, was working side-by-side with Killer Moth for a short while before Moth realized that his partner was dangerously insane (believing that he could see visions in flames, among other things) and promptly cut all ties with him.
In an issue of Gotham City Sirens, Poison Ivy tied up and gagged a nosy coworker who had threatened to reveal her secret identity to the police. Ivy initially planned to kill the woman in order to silence her permanently, but instead released her upon learning that she had a young daughter.
Joker's sidekick Harley Quinn is generally far less violent than Mistah J when left on her own, and never killed "innocent" people in her solo series or the Harley & Ivy stories. She stopped Ivy from executing the C-list heroine Thorn after she attacked them, instead convincing Ivy to leave her hanging Bound and Gagged from a statue. Then again, this had an added Cruel Mercy aspect since Thorn was left thoroughly humiliated after being discovered by the local citizens.
There's also a story from Batman: Black and White where Harley and Ivy rescued a little girl who was being pursued by a sexual predator. They promptly kicked the guy's ass before Batman even had a chance to show up, and the girl was left completely unaware that the women who rescued her were homicidal supervillains.
Johnny does have a standard that isn't used in that scene, however: He never harms children (intentionally). He also seems to be protective of his neighbor Squee, in his own warped way, especially when he rips apart the pedophile who's taken Squee out behind the mall.
"You flaw. At least I'm under the delusion of doing something productive."
Hunter Rose, protagonist of the early Grendel stories by Matt Wagner, was a sadistic, sociopathic crime-lord/hired assassin, who made a point of suppressing all underage prostitution within New York. In his first ever appearance he cheerfully guts the head of the largest child prostitution ring in the city, commenting "I no like dat."
Also, he will not kill in front of a child, even if it leaves witnesses to one of his crimes.
In West CoastAvengers, this leads to the defeat of the Lethal Legion. The villains are more than happy to engage in things like murder and kidnapping, but end up turning on their boss Grim Reaper after it's revealed that he's a racist.
In Geoff Johns's mid-2000's run of The Flash, Captain Cold violently beats his fellow Rogue Mirror Master for using cocaine. Justified in that he wants to run an efficient ship, and drugged-up partners aren't very conducive to that.
Captain Cold has a record of this: during Identity Crisis, he was noted to have sent flowers to the funeral of the murdered wife of superhero Elongated Man. He's generally been portrayed as viciously mercenary, but strictly professional. It's never—well, rarely—personal.
He and the Rogues also stop cold during the middle of a robbery when they find out about it. This is partly because they knew that superheroes would be on the rampage after Sue's death, but it was also out of respect for one of their foes.
Cold also mentions breaking Axel (Trickster II's) ribs and docking his take after he caught the kid tying bombs to dogs and homeless people to make snuff films. Axel's a bit of a psychopath, Len tries to keep him... straight... ish.
Mirror Master himself, despite being a merc/assassin (and apparently an on-again off-again cokehead), will not kill children.
Most of the Rogues have some line they won't cross; Gorilla Grodd, Kadabra and the Reverse-Flashes are the exceptions. It's mentioned several times that the other rogues do not consider these homicidal maniacs part of the team.
It's one reason the Rogues keep to themselves. When Libra was recruiting other supervillains to join his team, the Rogues turned him down. They just steal stuff—mass murdering of superheroes and civilians isn't their game. (Though this may have to do with Pragmatic Villainy.)
In one Silver Age story the Trickster breaks into a hobby store and weaponizes three of the toys in stock to use in robberies, but goes to the trouble of going in the next day and buying them (instead of just walking off with them while he was there) because he's "not a mean man." Subverted in the same story, combined with Hypocritical Humor, when he comments that, not being a mean man, he wouldn't normally endanger civilians — but it's worth it to distract the Flash, who will save them all anyway.
In another Silver Age story, Captain Cold is offended that Heat Wave served his sentence and was released on parole instead of breaking out — "If there's one thing I hate more than a straight man, it's a crook that pretends to go straight!" To take revenge, he plans to trick him into killingBarry Allen, because Heat Wave will be demoralized and easy to capture once he realizes he murdered an innocent.
In Forever Evil, Cold and the other Rogues raise up a rebellion against the Crime Syndicate after they order the destruction of Central City. The Rogues may have no qualms with conquering the world, but they sure as hell aren't about to kill a bunch of innocent women and children to make it happen.
In the same event, Captain Cold ends up in an Enemy Mine situation where he has to team up with Lex Luthor, Bizarro, Black Adam, and Black Manta. He is visibly disturbed when Black Manta implies that he wants to make sure the members of the Crime Syndicate suffer as much as possible before they die.
Black Manta: Your gun will make them numb. I don't want them to be numb.
Captain Cold: You have issues.
Black Adam gets this treatment as well. He may be a murderous Anti-Villain, but he does not take kindly to tyrants and dictators.
In the Age of Apocalypse timeline, Wolverine's nemesis Sabretooth pulls an epic Heel-Face Turn and becomes a well-respected superhero. He still started off as a pretty bad guy, but realized he'd had enough upon learning that Apocalypse planned to kill off the entire human race. (It should be noted that in this reality Sabertooth was less animalistic and frenzied than his standard counterpart.)
While not going so far, Mister Sinister is also disgusted in this continuity by Apocalypse, who he considers unnecessarily barbaric, and by Dark Beast, who he disdainfully regards as a petty sadist.
He also kills a psychiatrist who took advantage of a troubled teenaged client, which resulted in her committing suicide. He did the job for free, and was completely serious throughout pretty much the entire story and grew quite pissed when he began talking about it. The moral? If Deadpool's inner voices ain't around and he's being completely calm and serious, someone has done something even he wouldn't do. And he's not gonna kill them, he's gonna FUCKING MURDER THEM.
In the Deadpool vs Carnage arc after he finds the bodies of a couple and their children whom Carnage had taken hostage and murdered, he mentions that while he and Carnage are both crazy he would never do something like that.
The Teen Titans foe Cheshire, in her earliest appearances, did have standards. One issue had her hired by a white racist to murder a black civil rights leader who was pushing to end Apartheid in South Africa, with the added insult of then framing her victim as a Soviet sympathizer. This would effectively tarnish his reputation and lead to other black activists being discredited and killed, thus bringing the civil rights movement to a halt. However, upon killing the activist, Cheshire instead planted the evidence on her own employer, leading to his arrest and execution for treason, as well as the murdered activist becoming a martyr. It was earlier implied that Cheshire's own racial heritage (being half-Vietnamese) lead to her obvious discomfort over being hired by white supremacists.
Time went on, however, and Cheshire apparently decided that to get what she wants, maybe she shouldn't have standards. Amongst her later career, she literally detonated a nuke in a Middle Eastern country, manipulated Catman into getting her pregnant, and announced she didn't care that her daughter could be killed for her employer due to said pregnancy as she would still have a child afterwards.
The latter incident however seems to have been Retconned to an extent, since she was absolutely devastated and vengeful when her daughter didactually die. Either that or she was bluffing when she said she didn't care about her in the first place.
An Action Comics story had her assuring a Bound and Gagged hostage that she had zero intention of harming him since he had nothing to do with the actual assassination she was hired to commit. So at least at first, she tried to steer clear of harming innocents during her murders.
Carnage, as mentioned before, is probably one of the most insanely ax-crazy villains in the Marvel Universe. That being said, he still gets seriously pissed when he sees people parking illegally in handicapped spaces. His method of dealing with this is to attack and cripple the person, therefore making it okay for them to park there. Seriously, don't park in the handicapped spaces if Carnage might be in the area and you don't have a handicapped placard.
Set up to be Lampshaded, when Luthor decides on members for his new Injustice Gang. Cheetah objects to recruiting Doctor Light because he was a rapist, but Luthor dismisses this reasoning, stating that "if we want to limit our membership to people of good character...". Later, Cheetah has Dr. Light at her mercy, and evokes this trope... sorta:
Cheetah: Did you think I would work with a rapist without there being consequences?!?
Dr. Light: But... you're... you're a murderer...
Cheetah [raising her claws to eviscerate him]: Do as I say, not as I do.
In the late Bronze Age story "The Einstein Connection" by Elliot S! Maggin (a writer who had a definite soft spot for the original Mad ScientistLex Luthor), we learn that one of the few people the brilliant Luthor unabashedly considers a personal hero is Albert Einstein. While fleeing Superman at one point, he passes a body of water and sees somebody drowning. Though grumbling about it, he dives in and rescues the person, even though it costs him his escape, because he just can't bring himself to act like an S.O.B. on Einstein's birthday.
This became a subplot in Final Crisis with Luthor and Dr. Sivana. Originally in league with Libra, both quickly started covertly planning against Libra when they realized the true extent of Darkseid and Libra's plans. Lex decided he rather liked life (as opposed to anti-life) and Sivana said watching his own daughter submit to the Anti-Life Equation was the last straw. Libra's statement that leading the rearguard would grant Lex first line in what was implied to be a rape train on Supergirl probably helped to push Lex to find his moral fortitude as well.
In Grant Morrison's JLA, Luthor physically struck the Joker after the villain openly mocked a group of innocent children who had accidentally been killed during the Injustice Gang's attack on the Justice League. At the end of the story, Lex used the Rock of Ages to resurrect the dead children, with the justification that he could no longer be charged for any crimes if his victims were restored to life. Superman didn't buy this for a second, and told Lex that he knew he did it because he felt bad over the children's deaths, proving that deep down, there is some good in him.
Modesty Blaise, during her criminal career (the series starts when her retirement becomes too boring) was always very strict about rejecting drug-dealing and prostitution, and no violence against innocents was allowed. In fact she often did pro-bono attacks on procurers. And when she was set up to traffic drugs in return for the life of a friend, she chose NOT to traffic drugs. She was also against killing, unless it was absolutely necessary, preferring to knock out people who got in her way. Also, she gave her henchmen pension funds, when she retired her operations. It's hard to consider her a villain at all.
In the final Ms Tree stories, when the title character is heavily pregnant, there are multiple attempts to kill her. The current head of the Muerta crime family, who now considers the detective family because of her stepson's strong relationship with his niece, confronts the man who commissioned the attempts and tells him that had he known that Tree was the target he would never have agreed to it. However, what really sets him off is Tree's current state; he roars, "You tried to kill a pregnant woman, have you no shame?!" and immediately orders his goons to kill him.
The attempts were because the baby was not the son of Ms. Tree's deceased husband, but of a rebound lover, and therefore eligible for a chunk of inheritance that the would-be murderer wanted all for himself.
In the retelling of "Sleeping Beauty" featured in Castle Waiting, Satan himself proves to have standards. Disgusted with the evil witch being willing to curse an innocent baby then subvert the attempts to get around her curse, he disguises himself as the Opinicus (a griffin-like creature) and carries her off to Hell personally. The demon Leeds complains that he loses more friends that way.
In many cases, there are Decepticons in Transformers who are despicable even by Decepticon standards and roundly viewed with abhorrence by their comrades. Like the cannibal Skullcruncher, who devours downed enemies solely for symbolism (as he can't get nutrients from eating other Cybertronians and doesn't care for the taste, though he's occasionally been said to be able to regenerate faster doing it), or the especially cruel and bullying Motormaster. There's at least one Autobot who goes above and beyond Decepticon standards. Repugnus is... special like that... Repugnant.
Sunstreaker, who was actually diagnosed as a sociopath in one profile. Or Blaze Master who laughs as he burns Decepticons alive. Or Arcee who in the IDW books is a mass murdering torturer who likes to slowly kill her enemies. As the series has evolved Grey and Grey Morality has definitely emerged.
In the final issue of IDW's All Hail Megatron limited series, Thundercracker spoils Megatron's plan to nuke New York City because he felt that the Curb-Stomp Battle of the Decepticons against the humans was beneath the Decepticons' standards.
Megatron could arguably be at his most evil (and most good, for that matter) in the IDW comics, but when Thunderwing showed him his method of creating Pretender shells, which consisted of using living Transformer tissue, it was so horrific that even he rejected it and called Thunderwing mad. (He also fought alongside Optimus Prime against Thunderwing, when the scientist's self-experimentation resulted in him becoming a completely insane engine of destruction.) In addition, Razorclaw was ordered by Megatron to destroy Cybertron to stop Thunderwing; Razorclaw disliked the idea enough to put in a killswitch on the device that would disarm it if they could stop Thunderwing within a certain amount of time.
Aside from Swoop and Sludge, the Dinobots are also often portrayed as being Jerkasses (Snarl), bullies (Grimlock), or out-and-out sadists (Slag), and the shy Swoop and amiably dim Sludge cross into these areas at times... but while some treatments have them considering it, they haven't ever actually joined the Decepticons.
In Transformers: Last Stand of the Wreckers, Snare eventually rebels against Overlord's insane reign over Garrus-9 after being forced to recycle a dead Autobot and watch the execution of Rotorstorm. Snare was part of Stalker's torture team only a short while before.
Transformers Windblade: Nobody likes Starscream, even the Decepticons who served with him. Octane, who once almost nuked New York, feels he's a disloyal Dirty Coward, and Swindle, famous for double-dealing, manipulating, and generally swindling, thinks that Starscream treachery is too much.
While not quite evil, Sistah Spooky pushed aside her severe dislike of Empowered to warn her of an upcoming Humiliation Conga. Even she didn't like seeing what had happened before happen again, even to Empowered.
This behavior is justified for the "average" villains. There are what are called the "unwritten rules" about how a villain should treat captured superheroes (most notably, no killing or raping.) These rules are followed because any villain who breaks them is going to get the normally divided and unreliable super-hero community to band together and crush anyone who does. It's not standards on the part of the villains (Well, except for Wet Blanket), but rather simple pragmatism. Villains who do break these rules have the power to succesfully fight off massive teams of superheroes singlehandedly. This leads to the bizarre dichotomy of villains either being Silver Age style, or something that is The Joker at his worst. Only made of fire.
In Incredible Hercules, Hera, currently running the Olympus Corp, has a plan. A big plan. As of the writing of this entry, we don't entirely know what it is. What we do know, though, is that Norman "Green Goblin" Osborn, one of the ultimate dog kickers in Marvel as a whole, is downright aghast when he finds out what it is! If the man who is turning the world into his own personal oyster, and taking numerous baddies along for the ride, sees something as going too far, then that should be ringing a multitude of alarms.
Turns out it was the destruction of this universe in favour of one of Hera's own creation. No wonder even Norman couldn't stomach that.
Secret Six, a comic about a team of supervillain mercenaries, gets quite a lot of play out of the fact that, while they're all evil, the main characters all have different standards. In one issue Deadshot shoots an escaping slave in the back.
Deadshot: She ran, I shot. I don't know what you want from me.
Bane: Murdering slaves? Have you no scruples at all, mercenary?
In a Dragon Magazine Nodwick strip parodying D&D's "Slave Pits of the Undercity" module, evil slave lords Blackthorn and Markessa are shocked, appalled, and disgusted when Artax pretends to be a merchant seeking slaves to staff his chain of convenience stores.
Piffany: I told you: even they have standards!
Saga: When The Will kills an alien child sex trafficker.
In Watchmen, The Comedian, known for beating and attempting to rape the first Silk Spectre and shooting a pregnant woman who was carrying his child (in the stomach), is horrified when he discovers Ozymandias' plans. Since Comedian was at best a sociopath who, by his own words, saw life as one big Nihilistic joke, another interpretation is that what terrified and upset Comedian was less the lives lost, but more the possibility that Ozymandias' plan would succeed and create a world that he would have no place in.
He is also appalled when Sally insinuates that he would want to commit incest with his daughter.
Sally: Are there no depths you won't sink to?
Comedian: Jesus Christ Sally... Can't a man talk to his... Who do you think I am?
Dilbert example: Phil, the Prince of Insufficient Light and former ruler of Heck, looks for a job.
Phil: I would probably be good at any job involving sin.
Before Parker Robbins become The Hood, he was a thief, liar and supervillain fan who seduced and knocked up a gorgeous girl, and was cheating on her with a Russian prostitute. His cousin, John King, is an alcoholic who never worked a single legal job in his life. But when an agent of terrorist organization HYDRA offered them a job, they told him about how much they hate terrorists, beat him and stole his shoes.
Would have stolen the suit but John pissed on him.
In Legion of Super-Heroes: Legion of Three Worlds, when Superboy Prime frees all of the villains held captive on the prison planet, a temporary truce is called and all internal politics are abolished until the Legion is dealt with. However, the vast majority of the inmates make it very clear that once this is all over, they're coming for fellow prisoner Earth-Man and his Justice League of Earth, a gang of Terran supremacists who are essentially the 31st century version of the Aryan Nation.
In X-Force (the team that later became X-Statix), while the team isn't evil they're certainly amoral. However, when they see the patently insane and violent (even by their standards) Corkscrew making his way through team tryouts like a pro, it's decided that the only option is to have Doop take him out back and murder him with a logging axe.
If you're a Grandmaster of the Dark Legion, expect to face off against this trope eventually; former Omnicidal Maniac Dimitri has a lot of these, ever since his depowerment, most notably his balking at reviving his previous Superpowered Evil Side Enerjak, even though it would've restored him to health (even going so far as to warn his enemy Knuckles of Enerjak's return); and his usurper and current Grandmaster Lien-Da, who has no problems with performing Klingon Promotions and Mind Controlling the Legion as a way of gaining status, or torturing a former ally to death with a smile on her face, turns on her ally Shadow in the Mobius: X Years Later storyline, after it's revealed he's going to destroy the world with an Eldritch Abomination.
In Sonic the Hedgehog/Mega Man: Worlds Collide, Dr. Wily is shown to be bothered when he finds out that the Roboticizied Masters, which Dr. Eggman helped make via Sonic's friends and an altered roboticization process, have no real personality. The final straw for Wily is Eggman's attempt to kill Dr. Light. The revelation that the Super Genesis Wave could potentially destroy both their worlds didn't sit well with him either, Eggman assured him that they can rebuild their worlds however they want, making the damage irrelevant.
Upon his Face-Heel Turn, Geoffrey St. John admits in issue 235 that while he isn't always trustworthy, he does respect his adversaries. He even admits that what happened to Sally and Antoine isn't what he wanted and sympathizes with Sonic over what happened with Sally. He's horrified to learn in Universe 43 that Naugus plans Mass Hypnosis over the Acorn Council, an equivalent of roboticization. He believes that some lines need to be crossed to make things change, but Naugus' plan just goes too far.
Wonder Woman foe Dr. T.O. Morrow eventually turns against his own creation Genocide and works to help the Amazons defeat it, because he's of Polish ancestry and doesn't want anything to do with a creature who is the personification of genocide.
In the twelfth ever issue of Daredevil, Matt Murdock happens to be on the very cruise ship boarded by fearsome pirate the Plunderer. After changing into his Daredevil costume and pounding the Plunderer's goons, he makes a break for the man himself. But the Plunderer's taken hostages and threatens to toss them overboard into the shark-infested waters unless Daredevil surrenders. Not willing to risk their lives, DD relents, and one of the Plunderer's crewmen suggests tossing him overboard instead. The Plunderer is positively outraged at the very suggestion: "Silence, you scurvy toad! I have given myword!" For his part, Daredevil is impressed.
One Daredevil graphic novel has a mob boss refusing to let the Mafia make money from rackets such as drug-dealing and child prostitution; the mob may be criminals, but they aren't animals. Unfortunately for him, his consilgiere is Wilson Fisk, better known as the Kingpin, who snaps his neck and takes over. It's implied that Fisk was actually privately encouraging the guy to take a stand on this issue, just so he could have an excuse for his murderous coup.
Kingpin has been the subject of flip-flops of epic proportions: either he thinks drug dealing is rock bottom, or he's single-handedly keeping about half the world's drug barons in business.
In an early issue of Matt Fraction's Invincible Iron Man, Ezekiel Stane murders a bunch of tobacco executives after explaining to them that, even if he makes of weapons for terrorists and psychos, is disgusted by how they make their money.
Ezekiel: I might deal with murderers, but you guys — you guys are addicting kids and murdering them yourselves.
Though given what Ezekiel gets up to in that story arc, it's pretty obvious he's kind of a hypocrite, even if he did mean that seriously.
In the Fantastic Four Unlimited from July 1995, the villian Maelstrom is willing to destroy the universe... but not his own son.
Maelstrom: But— I'll NOT slay my own offspring!
Ant-Man: I can't believe this! Maelstrom— going paternal on us!?
Parodied in Runaways with Chase's mom, who reacts with horror at the suggestion that she get an abortion, saying it would make her a monster... while standing in front of the human sacrifice she is about to make in order to bring about the end of the world.
In an issue of Marvel Adventures Spider-Man, the Grey Gargoyle is commissioned by a wealthy client to steal the Venus De Milo, once he returns with the stolen statue, the client has one more job for him; to petrify a kidnapped super model so he can chop off her arms and put them on the statue. The Gargoyle responds by apologizing to the young lady for what she's been put through then petrifying his former client before he leaves.
In Garfield: His 9 Lives the Incredibly Huge Galactic War Fleet claims to have no hearts. However, they do "appreciate a tidy ship," and so give Garfield two extra minutes to get his spaceship cleaned up before they atomize him.
Given that Doom has frequently shown outright paternal feeling for the Richards kids (particularly Valeria) himself, he probably figures he could raise them better himself.
Doom also has no tolerance for racism. In the graphic novel Emperor Doom, when he finally succeeds in taking over the world, one of the first things he does is end apartheid in South Africa. Which makes sense given that his mother was Romani, an ethnic group that is still routinely persecuted in many parts of Europe.
In the original Alien vs. Predator comic miniseries that kicked the crossover off, the clan leader kills one of the younger hunters when he sees a child's skull in the other's trophy bag. That is part of the Predators' code—only those who can defend themselves, otherwise it's not sporting.
In one issue of Simpsons Comics, Mr. Burns tricks Homer into starring in a deadly gameshow. While Homer struggles to get through a maze full of traps, Burns sits in a control room pondering what to throw at him. We're shown some very dangerous and downright cruel things... but he draws the line at making Homer listen to James Cameron's infamous Oscar acceptance speech on a continuous loop, as he's "still a human being".
Marvel MAX Bullseye is one of the few people you wouldn't expect to have standards, seeing as he's done many horrifying things over the course of his self-titled arc in Punisher MAX, even the deaths of four different families in just a week, consisting of a wife, a son and daughter, slaughtered to reenact the death of Frank Castle's family, so he could feel how Frank feels.. But he, of all people, is not a fan of smoking.
In an issue of Spider-Man, Jason Macendale (aka the Hobgoblin) tries to sell his soul to the demonic N'Astirh in exchange for increased power. N'Astith responds by laughing in Macendale's face, telling him that his soul is so warped and disgusting that not even a demon would want to buy it.
In the Wolverine story The Adamantium Men, Wolverine and his rival combatant (part of a twelve-man mercenary team, employed by Blackguard and made to emulate Wolverine with laser claws and nanite healing factors) are busy fighting in the streets of San Francisco. The two have by this point fought all the way to street level and are about to deliver what might be the deathblow, when they see a schoolbus full of young children. To spare them from harm (and the trauma of their very violent combat) they retract their claws and let the bus pass, then choose to move in case another one passes. The rival was dishonourably discharged for unknown reasons.
It gets a bit confusing when you remember that at the very start of the issue the team were shown killing three children. Admittedly the rival may not have actually been there.
In Batman Incorporated, one member of the blue-collar crime gang Joe Average and the Average Joes gets very annoyed when it's suggested they have a connection to the similar French group Les Stereotypes, who run a child-slavery ring.
In the first crossover between Spider-Man and Superman, Lex Luthor and Doctor Octopus join forces to create a worldwide hurricane, to blackmail the planet for ten billion dollars. Eventually, however, Luthor reveals that no matter whether they get paid or not, he's going to let the storm run rampant and wipe out humanity to pay them back for laughing at him. This is too much for Octopus, and he smashes the machine generating the hurricane.
Using The Wasp as a living bomb was apparantly too much for even Norman Osborn and Bullseye. When the whole force of Marvel's heroes charged the Skrulls in vengeful rage, they joined in, looking just as pissed for what just happened as the good guys.
In a one shot issue of The Amazing Spider-Man illustrating the aftermath of the September 11th WTC terror attacks, Doctor Doom, Kingpin and Magneto turn up to help with the rescue effort at the World Trade Centre along with all the heroes, and superheroes. This drew criticism, because some of the villains featured have been shown to do worse or as bad as that. One of them was Juggernaut, who's actually attacked the WTC himself in the past.
In the Italian Disney stories about Paperinik the Devilish Avenger (Donald Duck's vigilante secret identity), Paperinik has committed his fair share of crimes (his first story sees him stealing Scrooge's mattress while he's sleeping on it, and he beated up and humiliated other characters and the police many times, even throwing Gladstone down of the wall of a castle before the whole population of Duckburg), but he always drew the line at gratuitous crimes and actually profiting from them (at worst he forces people who stole from him as Donald to pay him back more money than they stole from him), resulting in him capturing and handing to the police about half of Duckburg's criminal population.
In Peter David's "Countdown" story arc in The Incredible Hulk, the villainous Leader, who once gamma-bombed a town of 5,000 people just to see how many would survive (answer: five), states that he can't bring himself to kill his own brother.
Darkseid from DC Comics seems to fall under this. Despite being one of the most evil beings in existence, he does keep his word, such as letting Batman and Supergirl go during the Supergirl arc of Superman/Batman when Bats threatened to destroy his planet. That said, it didn't stop him from coming down to Earth to royally fuck up Superman, who was not part of the deal. There's also the whole deal with trading sons as a peace treaty. He'll find a loophole, but he usually doesn't betray his deals or promises. Then there was the fact that he threw the villain Sleez, who would later go on to try and make a porn movie with an unwilling Big Barda and Superman, out of Apokolips for being such a creep. (Note that he kicked Sleez out of Apokolips while he was still called Prince Uxas, before he truly ruled the place. If he had, it's doubtful he would have let the creep live.)
Knights of the Dinner Table Illustrated : Knuckles captured a member of the cult that tortured Thorina. Knowing that Knuckles intended to kill him, and knowing also the Untouchable Trio's notorious reputation for greed and selfishness, the cultist tried to persuade Knuckles to join his cult instead, offering lavish rewards. Knuckles mentally pictured himself torturing Thorina, and then promptly killed the cultist, saying, "Sorry, bud, but even I've got standards."
For a very long time, Spider-Man villain the Lizard was unable to harm Billy Connors, the son of his human alter ego. This is no longer the case, and the Lizard devoured Billy later.
Another Batman Example. The Broker narrates an issue to himself in Streets of Gotham. He's a businessman who buys abandoned properties and sells them to super villains for evil lairs (He also has the woman who provides the image for Ineffectual Sympathetic Villain fix the lairs up), he treats his employees well, and works on the standards of privacy and discretion, he also says you need to give to get in Gotham. He also says, that he just sells the things, he doesn't need to know what goes on in them. He mentions how Catwoman, Joker, and Mad Hatter are easy to deal with, but then there's Mr. Zsasz. He's the only man who makes the Broker want to reconsider his job. When he sells Zsasz a meat cutting facility, he sees children in cages begging for him to help them. He takes his money and leaves to go home and try to forget the experience. When Batman demands to know Zsasz's whereabouts, The Broker displays a different set of standards, and how he would never willingly divulge a customers business, no matter how he feels about them. After he's beaten up and Batman takes his records, it's implied that he wanted that to happen, as you have to give in order to get in Gotham, he thought the beating was payment for the information, and he would lose business if people found out he gave out the information without a fight.
In American Flagg, Titania Weis, a devoted fascist and member of an explicitly Nazi-inspired political party, objects to plans by the even worse American Survivalist Labor Committee to kill the entire population of Chicago with poison gas.
The Powerpuff Girls #57 (Feb. 2005): In "Presents Of Mine," Him persuades Buttercup into using her share of the girls' allowance (with which they planned on buying something for the Professor) into buying something for herself. But when the Gangreen Gang starts stealing toys from a charity bin, it cheeses Him off ("Even I wouldn't stoop to something that rotten!") and he helps the girls lay an unholy smackdown on the Gang. (And this is a villain that is supposed to be either the Devil himself or something very close. Go figure.)
In Infinite Crisis, Vandal Savage quits the Society when they attempt to have his daughter Scandal killed for refusing to join up with them, though given that Savage was perfectly okay with arranging for her to be raped to impregnate her with an heir for him, this was probably less about morals and more about pragmatism.
Although Judge Dredd is willing to commit nuclear genocide in the name of the law, he will not stand for discrimination of any kind. An example of this would be the story where he forces Mega-City One to change its policies on Mutants.
In The Mighty Thor, even though Loki wants to take his father's crown and rule Asgard, he does not take kindly to anyone trying to destroy it. Asgard is still his home, after all.
Way back in Rom Spaceknight, the Skrulls turn out to have limits, too. They pull a Big Damn Villains and save a town from the Dire Wraiths because they hate Dire Wraiths more than anything else in the universe.
The Big Bad of Trolls De Troy, when he learns what Waha's biological mother has in mind for her daughter (she's a prostitute turned madam and wants Waha to follow in her footsteps), decides to throw her off his dragon's back to her death far, far below.
During a prison break in Thunderbolts, The Juggernaut is offered a chance to kill a guard who has been captured by two of the inmates. Juggy states that murdering a scared, unarmed man with no powers is beneath him, especially since there'd be no sport in it. He convinces the inmates to spare the guard, and then leads them into a trap.
In an issue of Avengers Academy, the kids end up in a fight with Spider-Man's enemies the Sinister Six. Mysterio orders Rhino to kill the students, to which the thug responds by saying even if they're superheroes, he's not about to murder children just to soothe his employer's damaged ego.
Red Hood and the Outlaws: Arsenal's most cherished memory? Hitting Rock Bottom and trying to fight Killer Croc in order to "suicide by Croc", only to have Croc realize this and tell him to get his act together. A scaled-up beast told Arsenal he was embarrassing, meaning there was no where to go but up.
Later Waylon Jones, a.k.a. Killer Croc becomes his sponsor in his Alcoholics Anonymous Program.
Another Killer Croc moment in the New 52 is in his Villains Month comic, where he savagely hunts down and kills a few crooked cops for the murder of a cop who was nice to him when he was a child. Croc may not hold much love for police, but he knows who his friends are.
In one Hulk story from the Nineties, The Hulk has been brainwashed by the Red Skull to believe that the Juggernaut (who is working for the Skull as hired muscle) is his father, thus turning the Hulk into his servant. The Hulk causes some serious damage in the subsequent battle against the Avengers, until the Juggernaut blows his cover by being too nice. All Juggernaut did was praise the Hulk for his fighting ability, but it was more kindness than Bruce Banner's father had ever shown.
One Annual of The Batman Adventures had a story where Scarecrow, under a new identity has started teaching at a local college and looked to be redeeming himself. Then he found out one of his prized students was and still is a victim of abuse, possibly rape, by her Jerk Jock boyfriend., that was enough to bring back Scarecrow and to show the Boyfriend that even someone who's obessed with other people's fear has limits.
In Sonic the Comic Robotnik's right hand man Grimer thinks Robotnik is going too far by trying to destroy Mobius, the second time Robotnik tries to destroy Mobius Grimer quits working for Robotnik.
Titania, a villain of She-Hulk and Deadpool, among others, might be murderous and violent, but she will tip workers properly. Not tipping would be rude.
This makes some sense when you consider that prior to being turned into a supervillain, Titania was a scrawny blue-collar girl who was constantly picked on and slaved away in menial jobs. She knows how hard life in the service industry can be.
In one Batman story, Catwoman teamed up with The Joker to go against a rich family whose members included a bitty Ill Girl. When Joker tried to attack the girl and harm her in front of her father and older brother, Catwoman got PISSED and attacked him, yelling that she was a thief and all but wasn't in the plan for cold-blooded murder.
In one of the later stories of Nemesis the Warlock, Big Bad Torquemada is sent time-travelling, where he eventually encounters his namesake (and past incarnation), often considered the face of the Spanish Inquisition. The historical Torquemada takes his namesake prisoner and starts torturing him, but the future Torquemada is impervious and instead happily regales his past self with stories of the things he has done in the future, using lessons building upon those of many of his past incarnations, but especially his namesake's and Adolf Hitler's. The historical Torquemada is horrified by the things he hears, and the fact of how he will be remembered in the future as a vehemently racist bigoted psychopathic monster, rather than the humble follower of God's creed that he has always seen himself as, leads him to a prominent Heel Realisation.
Venom (Eddie Brock) is notable for the fairly large amount of standards he has. Like the Rogues mentioned above, he refuses to ever harm innocents and resists the symbiote's more violent urges, though he unwittingly tends to cause loads of collateral damage in his fights with Spider-Man. He's also disgusted by his psychotic "son" Carnage; when Carnage first appeared, Venom was willing to set aside his feud with Spider-Man to work together and stop Carnage from hurting anyone else. This is all because in Brock's delusional mind, he's the "lethal protector" of New York and Spider-Man is the monster threatening the city.
Averted in Volume 2, Issue 4, when Red Mist guns down a group of children. Then proceeds to kill the main character's love interest's mother and father and gang rape her with 2 of his henchmen. Though one could argue that the way the first volume ended she wasn't an entirely sympathetic character at that point. On the other hand, the book doesn't make any effort to justify her rape. Well, one of his Mooks asked whether if it was really necessary. The others were outright disgusted with Motherfucker and with themselves, but they did as told. They outright declare that the rape was going too far, but again they don't do anything about it.
In the following issue, Vic Gigante tells Red Mist that his gang aren't getting any special treatment anymore, and that the Police force & the various mafia families are gunning for them now.