In a Very Special Issue of Shadow of the Bat that spoke out against drug use, Tim Drake tries to convince a group of kids at his school that they shouldn't use such things, only for the lead kid to provide the sensible argument that Tim does not have any right to forbid the kids from doing what they want with their own bodies and that equally harmful drugs like tobacco and alcohol are legal, so it is hypocritical to pull the "that stuff's poison" card. Though Tim does have a point in that kids generally are not allowed those things by law either, the kids come off as more reasonable than Tim does.
In Action Comics #176 "Muscles For Money," Superman decides to start charging money to save people. While it is certainly true that Superman was doing some reprehensible things (charging insane amounts, forcing people to sign contracts before he will save their lives, etc) the primary argument seems to be that Superman doesn't deserve any sort of reward for the good he does. The worst part is when Superman politely requests the $10,000 reward for two criminals he brought in only to have everyone declare him a money-grubber for it, despite the fact that this is a reward the police themselves had offered and which anyone else besides Superman would have been given happily. He even makes a very good argument for why he needs money: while he could easily create money, for example crushing coal into diamonds with his super strength, doing so would probably wreck the economy. The other characters have no good answer to this argument, but still insist that it's wrong and we are clearly supposed to side with them.
In Convergence: Superboy #2, after the Kingdom Come heroes face Superboy, he becomes angry and determined to fight them despite their pleas to work together. Everyone (even Dubbilex, who narrates the book) states how irrationally and angrily Superboy is behaving... except Superboy is right for several reasons. First of all, they attacked first, so their pleas for peace seem hypocritical and petty after they were the ones who attacked him with Kryptonite gas. Second, Superboy has no idea if these guys are Evil Counterparts to the heroes he's familiar with. Third, the only thing Superboy knows is that anyone who loses their fight will see their city destroyed. When he asks why the KC heroes (if they're so noble) didn't surrender right away, they say because they have a better chance of figuring things out. Except, there was no way they could have known anything about Superboy or his world to make that judgement.
When Jason Todd, the second Robin, returned in the "Under the Hood" series, his primary goal was to take down the Joker. Towards the end of the mini-series, Batman tries to justify the Joker's continued survival by revealing he fears that his killing Joker would make for a line that he can never uncross, leading to Batman Jumping Off the Slippery Slope and becoming nothing more than a Serial-Killer Killer. Jason, who has been set up as a murdering maniac now little different from the Joker himself, immediately shoots back a rebuttal about the fallacious nature of this particular argument, asking why taking exceptional actions to deal with an exceptional individual, a monster whose list of crimes should have earned him the death sentence a dozen times over or more, would lead to those actions becoming the new default. As he points out, he's not saying that Batman should start killing crooks at random, or even that he should start lethally pruning his Rogues Gallery in general. Just that Batman should do what the legal justice system fails to do, and put the mass-murdering, psychotic, irredeemably evil monster that is The Joker to an end. It's telling that all Batman can muster in response is an empty apology and an insistence that he can't do that.
Death of the Family sees Batman finally explain another reason why he is afraid of doing so years later: it is because he sees Gotham or the darkness of it, as his true enemy. He fears that should he kill the Joker, something worsewould appear. Given how the DC universe works, he may not be wrong. Then we find out there have been three separate Jokers and things become more complicated.
Another answer was earlier given during the Hush arc: Batman is tolerated by the police as long as he doesn't takes the decision to kill criminals into his own hands. If he ever decides to stop enforcing Thou Shalt Not Kill, even for the Joker, then Jim Gordon will consider him to have gone as mad-dog as the rest of them and arrest him (by any means necessary). Batman, acknowledging that he needs at least Gordon on his side if he's to maintain effectiveness in his war, obliges him.note Note, however, that Jim's argument was mostly symbolic; at this point in continuity he'd actually retired from the GCPD.
Similarly, in the Superman story What's So Funny About Truth, Justice & the American Way?, animated as Superman vs. the Elite, the Elite are depicted as homicidal maniacs already in the middle of Jumping Off the Slippery Slope — yet, like Jason above, they do make a very real point about how some villainous individuals should be met with lethal force, if need be, and superheroes shouldn't be afraid to kill if the job demands it. Really, the only reason not to agree with the Elite is that they kill non-powered enemies who pose no threat to them, which to the average comic fan sounds like the writers are throwing out the baby with the bathwater rather than admitting there's a middle-ground.
The animated adaptation muddled things even further by adding Atomic Skull - a supervillain and unrepentant murderer who couldn't be incarcerated through any conventional means. The first thing Atomic Skull does after escaping from a high-security prison was kill one of Superman's supporters, leaving his son grieving and begging for retribution. Manchester Black steps in and blows Atomic Skull's head off, permanently ending his reign of terror while Superman does absolutely nothing simply because he doesn't want to get his hands dirty.
Manchester Black: People don't want babysitters in spandex to spank them when they're bad. They want surgeons to cut out the cancers that fester in us and make sure they never come back.
In general, whenever someone considers or makes an attempt to kill The Joker, this is always considered a case of Jumping Off the Slippery Slope even though the Joker is the poster clown for Joker Immunity. For example, in Knightfall, Jean-Paul Valley, the temporary replacement Batman, stops one of the Joker's murder schemes and decides that he's going to be better at the job than Bruce and kill the Joker right away. The Gotham City Police Department pull their guns on Valley and tell him to stand down. Jean-Paul Valley was DC ComicsTake That! against the '90s Anti-Hero, so his actions were supposed to come off as too extreme, but Gordon and his subordinates place a ridiculous amount of faith in a justice system that has been demonstrably corrupt and/or inept. Almost to illustrate that point, five minutes after the Joker is arrested, he kills his guards and escapes in an ambulance.
Superman Annual #3 depicts a Bad Future where Lois is killed and Superman decides to bring about nuclear disarmament. This leads to him becoming more controlling and authoritarian, and being linked to the deaths of a few people (which weren't his fault), and so the government asks Batman to take him down in a fashion pulling heavily from Batman: The Dark Knight Returns. Batman is meant to be seen as in the right, just as he was then, despite the fact that he's now on the opposite side.
The Authority tended to do this to any critics of the titular team — except the Authority did tend to often act without regard for the consequences of their actions could effect others, and were often excessive and fascist in the way they acted (at one point, they overthrew the U.S. government). More often than not, their critics tended to actually have valid reasons to call the team out for their actions.
Films
Lex Luthor in Superman Returns accuses Superman of selfishly withholding the advanced alien technology he inherited from his dad, so that the planet is forced to stay dependent on Superman. While he is wrong about Superman's motives for doing so, he has a point. Sharing, say, what Kryptonian science knows about medicine or space travel or producing food would probably save a lot more lives than individually putting out fires with super breath. There are a few hints at an explanation in the first movienote there is some form of Alien Non-Interference Clause in place that prohibits Superman from interfering with human history, but the lack of detail of what is permitted, why it's in place and how this is supposed to be enforced — if it even has enforcement — leaves it somewhat lacking as a response (in addition to not being raised in the same film).
A number of characters have tried to force Clark/The Blur out of hiding and into the spotlight of the public eye. Since the series as a whole was building to Clark eventually coming out as Superman, the arguments for Clark staying hidden became less credible over time. The evil reporter from Season 2 who tried to forcibly expose Clark's secret argued that the public had a right to know about a powerful alien living in their backyard, which makes sense from a purely ethical standpoint of journalist ethics (as well as the aforementioned fact that the public would eventually find out about him), even if Clark does indeed have a right to a private life. There was also the corrupt DA from Season 9 who wanted The Blur to show his face and answer for a series of screwups that were blamed on him that were really the fault of the Wonder Twins trying to impersonate their favorite hero; his corruption was revealed last-minute as a means to give the Wonder Twins a heroic gesture and kill any debate on whether or not the Blur should have to reveal himself to clear his name.
In the early episodes, any interaction Clark had with Lex fell into this, and the one that stands out the most is "Memoria". Lex was trying to regain his lost memories from "Asylum". When Clark tried to stop him he ended up getting captured, and when Lex called him out on this Clark's only excuse was that in trying to stop his father Lex repeatedly stoops to his methods and innocent people get hurt. However, this falls on its face when you realize that the only reason Clark got hurt was that he was trying to stop Lex for, as Lionel said, his own selfish reasons. What Lex was doing only affected himself and that was his decision. Lionel wouldn't have known about it if Clark didn't get involved.
While it's true that Lex and Lana both became insufferably smug, they still had legitimate points when it came to protecting Earth from a potential Kryptonian/Phantom Zone/other alien invasion. In Seasons 5 & 6, Lex and Lana start sniffing around about Kryptonian technology, trying to learn everything they can about it. Clark gets very upset about this, but Lex and Lana repeatedly note that if aliens like Zod or Brainiac ever return, learning how their technology works just might end up being the thing that saves humanity from them next time, which is a perfectly defensible viewpoint. Indeed, Clark and the JLA themselves start incorporating bits of alien tech later on in fights against Zod and other threats.
Diana has dinner with a Senator who expresses concerns about the way she does things — namely, using Cold-Blooded Torture to get information from criminals, giving the metaphorical finger to Reasonable Authority Figures, and outright committing slander by holding a press conference to accuse Liz Hurley's character of being a murderous Corrupt Corporate Executive and admitting that she doesn't have any proof besides gut instinct. In fact, the only reason she's meeting the Senator is to get justification so she can go after Hurley. Of course, since Wondy-In Name Only is the hero of this story, she's ultimately presented as right.
Although the Senator's point about the press conference is redundant: imagine Superman calling a press conference in Metropolis and telling the world that he personally believes a particular series of mysterious deaths were directly caused by Lex Luthor doing things at LexCorp and that he is personally going to investigate it but that he has ZERO evidence at this point. This means that yes, Lex Luthor can complain to the authorities that the Kryptonian superhero (who may not even have another name or social security number) publicly slandered him but it also means that anyone else giving Luthor grief on the grounds that "Superman said you're behind it!" would also admit they are acting that way because Superman personally believes something while admitting he has no evidence of it.
In Batman: Arkham City, it's treated as a given that the player, as Batman, will stop the League of Shadows' plan to wipe out all the criminals locked up in the titular prison a la Protocol 10. However, the Enemy Chatter portrays the criminals as Card Carrying Villains who are only kept in line by their fear of their even worse bosses. The game shows what horrible crimes (including poisoning thousands of civilians with the Joker's blood, just to motivate Batman to find a cure) the criminals can commit from inside the prison. The previous game showed that therapy as it exists serves only to get the therapists killed, maimed, traumatized or brainwashed by their criminal patients. And neither prison nor asylum can hold Gotham's supervillains for more than 6 months, letting them rack up another big body count before Batman stops them again. Given the lack of viable alternatives to protect the people of Gotham from Batman's rogue gallery, the League of Shadows' plan begins to sound reasonable. Oracle even asks if standing back and letting the League do its work would really be for the worse with Batman only shaking her from that train of thought by pointing out that there are political prisoners that are only there because of actions taken against the League rather than actual guilt of being criminals.
Taking from the above in a sense, there's the DLC adventure A Matter of Family for Batman: Arkham Knight. The cops who Batgirl rescues through the story (which happens shortly before the events of Batman: Arkham Asylum and those inspired by The Killing Joke) all beg and vouch for Batgirl to kill the Joker for the stuff he's done to them. This is obviously meant to be seen as a wrong mentality since Batman and his allies don't kill criminals...but when one sees all the stuff that the Joker has done (the secret story of the amusement park's owner and her daughter and what the Joker and Harley did to them is nothing short of horrifying) and will do in the future to Barbara in particular, and all the death, suffering and horror that would come out of them in general, it may have been better to follow their advice and finish him off before he set into motion all the events of the series.
Superman in the first Injustice: Gods Among Us is meant to be seen as wrong for having killed the Joker (which led to his Start of Darkness and ended up turning him into a tyrant). In fact, people like Batman or Alfred in the comics give him the cold shoulder after this and Catwoman even treats him as a serial killer who can't wait to strike again. The problem is the same as in the other instances where the Joker is presented: he's the JOKER! And in this universe he managed to kill millions thanks to a nuke...while making Superman semi-responsible of all the deaths, including the deaths of Lois and her unborn child. This pushed him real hard into the Despair Event Horizon, in a way where no person, superpowered or not, could have maintained his sanity intact...and yet he's lambasted for not keeping the moral high ground despite the fact that the Joker more than deserved to be executed for his crimes (and most likely would have been anyways thanks to what he did). While it does not excuse all the awful things that Superman did later, it's pretty hard to blame Superman for killing someone who did something so horrid. Not to mention he was under a modified version of Scarecrow's fear toxin. The same toxin that causes people to act crazy and out of character!
Western Animation
Batman: The Animated Series: Lyle Bolton aka Lock-Up, during his stint as warden of Arkham Asylum, is an inhumane sadist who's quite proud of his extreme treatment of his prisoners. But not only did he kill Arkham's infamy as a Cardboard Prison, but his "victims" are mostly documented psychopaths who have endangered hundreds if not thousands of people over their time as criminals. After he gets fired, he comes across as a hard-headed conservative nutcase with his rant about the inefficient politicians and the "liberal media" being the cause of the superpowered psychos. While his blame might not be totally accurate, he's not wrong that no one is actually addressing these obvious problems. The police routinely fail to combat the maniacs, leaving a vigilante to do 90% of the work, Arkham is such an ineffective prison it may as well not exist, and no one in charge of the city or prison seems to actually care. The news even treats Poison Ivy as a media darling instead of an eco-terrorist (although in fairness as far as villains go Ivy is mostly pretty tame and mostly doesn't actually hurt people). If they all did their jobs more efficiently and professionally, maybe there wouldn't be so many costumed freaks terrorizing the city.
An example that occurred to the writers happened in the episode "A Better World". In it, Batman gets into a debate/duel with his Justice Lord counterpart, about the latter's seizing control of the world. Originally, League!Batman was meant to convince his counterpart, but after writing a particularly apt line for Lord!Batman note "You grabbed power!" "And with that power, we've made a world where no eight-year old boy will ever lose his parents because of some punk with a gun!" the writers couldn't come up with a compelling counter argument. In the episode proper, League!Batman concedes the point, and later gets through to Lord!Batman by pointing out how much their parents would have (dis)liked the new Gotham.
Eclipsed has Wally start using his Flash persona to make some extra cash, which leads to the league reading him the riot act on how he is 'selling them and himself out'. The problem comes when you realize that, unlike the rest of the league, Wally isn't already a Pulitzer class reporter or multi-millionaire or Princess. He's just a normal guy who spends a huge amount of his time on super-hero work already. While using his Superhero persona to star in cheesy energy bar commercials might not exactly be ideal, it's not actually hurting anyone and their implications that he shouldn't use his position to make ends meet falls a little flat. This is to say nothing of the fact that it wouldn't kill the organization that owns an orbital space station to pay their heroes a salary.
In season 2, G. Gordon Godfrey is an incredibly biased, inflammatory, and paranoid newscaster who constantly criticizes the Justice League unfairly, is suspicious towards aliens in general, spreads obvious misinformation and propaganda, and is revealed in the finale to be working for the villains. Unfortunately, his fundamental message of promoting public accountability of the League does ring true, however obvious it is that the heroes are in the right. The League keeps a lot of secrets from the public for arbitrary reasons; they don't even publicly announce a team member's death to avoid "people thinking we're mortal". They are an organization of superhumans and nonhumans responsible for the safety and security of the entire Earth, but they really aren't beholden to anyone except themselves. In more than a few ways the Justice League still acts like a secret group of vigilantes, despite being an extremely powerful public institution that consistently interferes in global affairs.
The ambassador of the Reach is likewise presented as a villainous mouthpiece whose words are poison, but he actually never makes a single accusation regarding the League that isn't both true and describing something that's extremely illegal for very good reasons. He stands out especially for pointing out that the basic premise of the series in itself makes the League guilty of a war crime that would get pretty much any other nation occupied by the UN.
Superman's initial treatment of Superboy comes across like this. We are supposed to see Clark's refusal to mentor and serve as a father figure to Conner as a bad thing. However, let's look at things from Clark's POV here:
Firstly, no matter what your view on clones are, Clark is right when he says he is not Conner's father because he quite literally isn't.
Secondly, Clark is on a reporter's salary and likely can't afford to take care of a kid right now, let alone one with super powers. Other heroes have advantages that Clark doesn't like Batman and his butler or Kid Flash actually having parents so the Flash doesn't need to raise him.
Thirdly, Conner is in the care of Red Tornado and Black Canary, so he doesn't need Clark as a caregiver.
Fourthly and finally, no one seems to take into consideration that Clark might not be comfortable around a clone that was created from his DNA without his knowledge or consent. A clone who was created to kill and replace Clark. On top of that, it's eventually revealed that Conner is also partly a clone of Lex Luthor, Superman's archnemesis, giving him all the more reason to not necessarily want to be within arm's reach of Conner when he would be vulnerable, such as while he's asleep, even if he might otherwise be sympathetic to Superboy's situation.
