An issue of The Ultimates had Batmanclone Nighthawk break his ankle trying to pull off a Dynamic Entry by jumping off a building to attack some mooks. The same issue it even deconstructs the concept of a Ragtag Bunch of Misfits by showing how badly a group of people (The Defenders), inexperienced at superheroing, with the exception of one, performs during their first outing as superheroes.
Old Man Logan revolves around a Legion of Doom wiping out the superheroes with sheer numbers after all the villains are able to finally put aside the personal differences that keep them apart in the mainstream continuity.
A teenager with no powers or special training decides to become a superhero. Especially when Kick-Ass fights crime for the first time he ends up getting stabbed by one of the thugs. Then subverted by...most of the comic after that point. To start with, getting stabbed and hit by a car gave him just enough, very specific nerve damage to stop feeling almost any pain.
The Tykebomb-turned-superhero Hit-Girl is clearly damaged by her upbringing, escalating into disturbing hallucinations of her father still giving her orders and advice.
Dave's pretending to be gay in order to get close to the girl he likes ends very badly. The girl is extremely pissed off to have been lied to and manipulated by what she thought was her Gay Best Friend, has her boyfriend beat the crap out of Dave in retaliation, and then later taunts him with pictures of the two of them having sex.
The second issue of Superior has a kid testing out the superpowers of his favorite Superman Expy. He attempts to use his "super-breath" to put out a house fire, only to demolish the house and spread the fire over a much larger area.
Similarly, the villain in Grant Morrison's Seven Soldiers event. Time-travelling jellyfish-totem Gothic Queen versus runaway car. The result is messy but suitably awesome.
One of Wolverine's greatest vulnerabilities is drowning, particularly as he is so heavy with his metal skeleton. If his brain suffocates, his healing factor can't do anything about that.
Speaking of Wolverine, it was shown that the reason why he got abducted by Weapon X in the first place was because he went binge drinking (even with his healing factor he's not immune to large amounts of alcohol). Sure, he may not have been drunk enough to fall over but the amount of alcohol in his system was enough to dull his normally fast reaction time. By the time he fought back against his abductors he was overwhelmed rather quickly and got cuts, bruises and a dislocated jaw out of it. In a What If? scenario involving Weapon X Logan managed to fight back and successfully flee his would-be abductors because he wasn't as drunk at the time.
Mainstream Doom is protected by a similar case of reality, only he's even better protected since he's the ruler of Latveria. Being in charge of a major, first-world country means that he can cover-up or get away with his attacks on the Fantastic Four pretty easily. Most governments aren't willing to start a war with someone just because they keep harassing four people.
Every time Wonder Woman and Batman go up against each other and Batman isn't prepared. These incidents typically end in Batman get flung off a rooftop or knocked out with a rock, simply because he can't carry weaponry capable of hurting an Implacable Woman like Diana on him all the time, and his agility can only help him so much.
In an issue of Avengers World, Shang-Chi draws strength from the tales of three warriors from Chinese history: A monk who fought off a squad of his emperor's warriors, a lawman who managed to defeat the assassin who poisoned him, and a peasant girl who single-handedly defended her village from a group of bandits. Despite the inspirational nature of the stories, Shang-Chi later notes that they all come with very unfortunate epilogues: The monk died of a broken heart after realizing he'd been betrayed by the emperor, the lawman defeated his attacker but succumbed to the poison while in a hospital bed, and the peasant girl was murdered after the bandits returned and attacked her while she slept.
One Spidey issue had the Vulture try to rob the Daily Bugle. However, he finds that their safe is full of paychecks, and the actual money is in the bank.
Also in Back in Black storyline, once Peter learns that the Kingpin was the one who hired the assassin that shot his aunt, he goes straight to the prision where the Kingpin was, but the Kingpin already expected that and is prepared to challenge Spider-Man in combat. While the Kingpin has faced Spider-Man before and often battled him to a draw, the problem is that Spidey always holds back in fear of accidentally killing him, but this time, hedoesn't! The result: Kingpin is quicklyand badly beaten. As it turned out, no matter how skilled hand-to-hand combatant or how strong Kingpin is, challenging someone who is superhumanly strong and agile, has experience in fighting far stronger opponents and is reallymad at you can't possibly end well.
Spider-Man was built on a deconstruction of superhero tropes. Because of his superhero activity, Peter Parker has a hard time keeping a regular job or staying current at school, and constantly is hurting for money as a result. Even sales of his photos to the Daily Bugle are subject to the needs of the paper. Peter also has to deal with the emotional stress of being The Unfavourite in his everyday life and (thanks to J. Jonah Jameson'ssmear campaign against Spider-Man) as a superhero, as well as caring for his elderly Aunt May (who is vulnerable both because she is old and sickly, and because she is Peter's—and therefore Spider-Man's—closest emotional tie). A lot of Spiderman's missteps in his early years (bad publicity, failed attempts at networking with other superheroes) are the result of what happens when a young teenager tries to be a superhero without a mentor or anyone else to help him, while also dealing with other stresses mentioned above.
In Common Grounds, a fight between a superhero and supervillain ends up killing a civilian caught in the crossfire. The result is both hero and villain getting arrested and sentenced to prison for manslaughter. After they get out, the hero ends up homeless and struggling to find employment, as it's difficult for ex-cons to get jobs.
In Uber, the American superhuman Colossus goes up against his Nazi counterpart Sieglinde. Colossus hasn't been fully enhanced yet, but he's brave, clever and determined...and the fully-enhanced Sieglinde rips him to pieces in a matter of seconds.
The Ax-Crazytitle character experiences a truly horrible example in a flashback from his early teens. From two miles away he hears his foster mother is about to commit suicide, and gets there in a fraction of a second, intending to stop her. But sound takes almost ten seconds to travel two miles. She had already been dead when he heard her.
When he reveals his Secret Identity to his Love Interest, instead of being awestruck by his awesomeness she's freaked out that he deceived her like that and wants nothing more to do with him.
The Runaways at one point have to fight a supervillain barely a week after they last caught him because they stupidly left him tied to a lamppost with a note for the police after the first battle. The guy easily got away the second the Runaways left. This is why most heroes like Spider-Man directly hand over villains to police or at least make sure they're securely trapped before leaving.
Amusingly one of the first times Empowered comes across as actually being badass. She points out, quite effectively, that driving an SUV at 75 miles an hour into a villain's back is much more effective than hitting him with a thrown one at about 5 miles an hour. This allows her to defeat a villain that the entire superhero squad she's a Butt Monkey for was defeated by. Unfortunately, the car is totaled, leaving her tied up and unable to brag, and her superhero squad walks off, assuming they and the villain knocked each other out. (Forgetting about Empowered in the process.)
This is the central premise of Watchmen: what happens to superheroes when Reality Ensues? What becomes of people who dress up in costumes but 1: They have no proper training or resources, 2: They're all at least a little unbalanced, and 3 (most importantly): They are taking the law into their own hands in a world just as full of political and social complexities as the real world? They die. They go insane (presuming they weren't insane already). Or they become monsters.
The first Nite Owl was a police officer during his day job, so he actually was properly trained and had official authority if he chose to use it. This is why he's the Only Sane Man among either generation of superheroes.
In his autobiography, he casually mentions that once the "costumed hero" phase hit its peak, most costumed villains simply gave up entirely or became regular criminals because, honestly, what's the point?
One hero was killed ignobly after his cape got caught in the revolving door at a bank. The robbers then simply walked right up to him and shot him point blank.
In The Boys the Seven find out very quickly that having superpowers doesn't automatically mean they know how to fight crime. Cue September 11.
In Ultimate Avengers the Nerd Hulk challenges a vampire named Anthony to a fight. Anthony agrees, and Nerd Hulk decapitates him with one punch. Hulk has Super Strength and doesn't have any reason to hold back against a vampire so...
Ant-Man: Season One tries to portray the realistic dangers behind an untrained person using Size Shifter powers. For instance, on his first outing, Pym is nearly killed and eaten by a spider.
The Transformers: A "virus" of smaller robots is released on earth, which quickly infect the Autobots and Decepticons stationed there. Several expendable Autobot prisoners are sent to earth by the Decepticons to spray acid on the infected. Instead, a cure is discovered, water. The water causes the small bots, Scraplets, to fall off of the transformers. The Scraplets then merge into a larger creature with a Hive Mind. Spraying it with water just makes the creature fall apart, but it easily reassembles itself. So the Autobots just free the Decepticons, who use their weapons to butcher, blast, and set the creature on fire. Miracle cure or not, shooting the damn thing was pretty effective. One of the formerly infected Autobots then grabs the acid and douses the creature with it, killing it for good.
As a result of his high exposure to radioactive Kryptonite, Lex Luthor eventually got cancer. Hey—human or superhuman, a radioactive rock is a radioactive rock. The irony is that it was thought to be without any effect on humans, except that Lex was exposed to more Kryptonite than any other human alive. Batman has the sense to carry his tiny piece of Kryptonite in a concealed lead-lined box. Lex, being an arrogant tool, just had to flaunt his Kryptonite on a ring.
The very first issue opens with this. Clint falls from a great height and manages to catch himself with a grappling arrow... but still suffers some pretty severe injuries and ends up in the hospital for six weeks.
Similarly, throughout the series Clint is constantly covered in bandages and injuries from his fights, and while a Badass Normal with experience fighting the likes of Ultron and Loki, he often ends up being taken down by mooks when they Zerg Rush him. Of course, it doesn't really matter how badass you are; being hit hurts and you can't always rely on Mook Chivalry.
The incident with Madame Masque, minor as it was at the time, leads to her becoming Kate's Arch-Enemy and devoting all her time and resources to destroying her as slowly and painfully as possible. Most superhero stories would ignore the fallout of such a minor confrontation, but this one goes to great lengths to show why pissing off a deeply disturbed individual like a costumed supervillain is probably not a good idea.
That same story shows the risk of breaking into a room through the window. All of those glass shards lying around hurt.
Another issue has Kate having to swim across a flooded street. She dives underwater with her eyes open expecting to be able to see semi-normally like people do in movies. Unfortunately for Kate, movies do that for audience benefit and she quickly realizes her mistake when all she sees is vague blurs and gets bad eye strain. Upon exiting the water she lampshades this trope.
More Kate Reality Ensues: When Kate moves to the West Coast, she ends up going against Masque's personal mooks, all by herself. Kate is a seasoned Avenger having worked with the Young Avengers and the main Avengers, and trains regularly with Clint. She's also a rather short, slimly built young woman who generally either fights enemies alongside a team or at least with Clint by her side. Just like Clint, she doesn't escape many fights without a lot of bruises and is quick to succumb to Zerg Rush tactics.
Dilbert joined a society dedicated to the preservation of an endangered squirrel. The idea was to tranq the last male and mate it with the last female.note Which wouldn't provide sufficient genetic diversity, but these guys aren't exactly geniuses. Dilbert's team get to work, they fire the tranq from the rifle from a few feet away, there's a Reaction Shot of their Oh, Crap faces, and then one of them points out that, perhaps, they should've used a smaller dart.
In Avatar: The Last Airbender – The Promise, a sequel to Avatar: The Last Airbender, the plot revolves around the fact that there will be a difficult peace process following a century-long war in which many people died and some land changed hands. Even if both sides are headed by well-intentioned individuals, there remains the potential for conflict to reopen.
During the Batman: Hush storyline, at the start of the story Batman's rope for his grappling gun is cut, causing him to fall toward the ground. He manages to grab onto a nearby statue... except that just causes his arm to snap like a twig due to the inertia of the fall. Then the old, worn-out statue breaks under Batman's added weight and Batman plummets into the alley below. He breaks his fall somewhat but still ends up fracturing or breaking half the bones in his body.
There's a very similar example in "Marshal Law Takes Manhattan", in which a psychotic parody of Daredevil is falling to his death from a skyscraper and manages to grab hold of a flagpole protruding from the building... whereupon the inertia rips his arms off.
In an issue of Superboy from the New 52, Superboy offers to fly a woman home. Shown from Superboy's perspective, it seems to be a normal trip, but when they arrive, the woman throws up and is extremely upset. Superboy then realizes that he flew at super speed without any thought to the fact that people aren't invulnerable or used to such things.
The final run of Punisher MAX shows us exactly what kind of a toll a 30+ year war on the criminal underworld can have on your mind and body. It makes you old, slow, arthritic, unable to shrug off injuries that would barely phase you years before, and that much more prone to slipping up. And the more you slip up, the less intimidating you are to the criminal underworld you hunt.
In an earlier arc, "The Slavers", The Punisher decides to attack a group of former Bosnian soldiers turned sex-slavers. A huge deal is made in earlier stories about how Castle's success rate owes mainly to his opponents being street hoods and armed thugs who're only good at intimidating people... but not this time. Castle quickly realizes his mistake when the men he's firing on quickly and methodically get under cover and start firing back, and is quickly forced to flee for his life. Turns out it doesn't matter how much of a badass you are: when you're facing combat-hardened soldiers, twenty to one are really, really bad odds.
In Forever Evil issue 1, Ultraman pushes the moon into the sun to create a solar eclipse. In Black Manta's Villain's Month issue, Ultraman's act causes tides to go wild; flooding coastal areas. This includes demolishing the graveyard where Black Manta's father is buried and he's not happy about that.
The Superior Foes of Spider-Man viciously subverts the idea of Punisher-style anti-heroes are somehow better at fighting supervillains simply because they're willing to "do what it takes". In the finale Shocker launches the Punisher into the horizon in a single panel. Frank might be The Dreaded but he's still a normal man who found himself up against a guy who could blow apart buildings with a squeeze of his fist. Earlier in the comic the other members of the Sinister Six effortlessly blast their way through the Owl's henchmen, as they're armed with high-tech weapons and superpowers and the mooks are just normal guys. How's a pistol or crowbar supposed to help you against potential lunatics wielding things like sonic gauntlets and super speed?
Superman by his very nature avoids most of these tropes, but his official authority is often an open question. The Man of Steel averts this by having the mayor of Metropolis (as fallout from a challenge to his authority by Lex Luthor) commission Superman directly as a special deputy, which at least gives Superman jurisdiction within Metropolis city limits.
In the earliest Golden Age stories, Superman would take on normal criminals and the corrupt and was more lax with death threats and property damage. However, in Superman in the slums even he's initially stumped as to how to fix juvenile crime in a dilapidated neighborhood since there isn't someone who's directly responsible. Of course he finds the solution and demolishes the neighborhood, after the people evacuate of course, once he learns that the government will build modern housing projects to replace the old buildings, but still.
In Spider-Man's "Death of Jean DeWolff" story, Spider-Man gives the Sin-Eater a No-Holds-Barred Beatdown. The next time the Sin-Eater appears, he's a stuttering, limping wreck as a result of the severe injuries he suffered. Adding to Spider-Man's guilt even further, the Sin-Eater's Insanity Defense led to successful psychotherapy, so the Sin-Eater is a genuinely remorseful stuttering, limping wreck.
In the first issue of All New Ghost Rider, Robbie Reyes tries to stop three gang members from stealing his brother's wheelchair. One of them pulls out a gun. You would expect Robbie to show what a Badass Normal he is, dismantle the thug with the gun and beat them all up. Instead, he stands still and the thugs beat him up and steal both the wheelchair and his shoes. This shows that, despite growing up in a bad neighborhood, Robbie isn't some sort of impossibly tough delinquent, but just a regular guy.
A few years ago X-Men character Fantomex saved the world from a monster brainwashing people into worshipping it as their god by revealing he is programmed to be incapable of conceiving anything greater than himself, therefore he cannot believe in any god. A 2014 issue of X-Force reveals that whenever he is outdone at anything, the same ability causes so much cognitive dissonance he ends on the verge of mental breakdown.
In a strange twist, the same issue showed that when one of the deities is away for a week, someone had to fill in for her so the world doesn't go into chaos. Luna had to instead raise the sun every morning for a week, because according to the reality of their universe the Sun doesn't raise itself. She also finds out that it wasn't as easy as it appeared.
In the Equestria Girls holiday special, even after Anon E. Miss is revealed to be the Cutie Mark Crusaders, who were posting details about students personal lives out of jealousy that Sunset Shimmer was getting more attention from their sisters than they were, and even after the apology is accepted by Sunset Shimmer, the things that Anon E. Miss posted online don't just disappear. Rarity even tells Sweetie Belle that it'll be up forever. Earlier in the story, Sunset laments to Twilight Sparkle how easy it is for someone's reputation to be destroyed with a few online posts.
In FoxTrot, Jason spends the cash prize from a chess tournament on gumballs. The next time he goes to the dentist, he has cavities.
The Marvel NOW! relaunch of Uncanny X-Men shows a neat subversion of the typical Fantastic Racism. While mutants are still facing a lot of bigotry, they're getting a lot of support now thanks to the progress made over all the time the X-Men have operated, and while hated by S.H.I.E.L.D. and the other X-Men for nearly taking over the world killing Xavier while under the influence of the Phoenix Force, Scott Summers/Cyclops is now getting a lot of Hero Worship because of his other actions, namely nearly solving world hunger, stabilizing the climate, and forcing peace between warring nations. As it turns out, it doesn't matter if you're part of a hated minority, when you nearly solve a lot of the world's problems, it nets you some serious brownie points (even if you were possessed by a big scary space bird at the time and your reasons for doing all these good deeds were at best questionable).
In Ultimate Spider-Man, Peter is knocked out while trying to take out Kingpin in the second story arc. Rather than tying him up or killing him, Kingpin has his mask removed to see his face, then has him thrown out a window. This bites Kingpin in the ass later, since he has no idea who Peter Parker is, and so seeing Spider-Man without his mask (and not bothering to take a picture) only leaves him with "White, brown-haired teenager".
Archie Comics' Sonic the Hedgehog: For the longest time, there were many factions and individuals that, based on their respective showings, could've defeated Dr. Robotnik/Eggman very easily. In particular, the echidna civilizations would've delivered a Curb-Stomp Battle if they fought him. Instead they allowed him to continue since he wasn't a serious threat to them and he kept the other minor threats under control, even though his schemes have endangered them one way or another and he was aware of them from his time in the royal court of Mobotropolis. He was able to to improve his technology to the point that, with some minor help, he could attack them directly and raze their civilizations to the ground. And now with the reboot, all of these people have been neutralized.
In one The Avengers story by Jonathan Hickman a group of supervillains has taken over a country and then sent one of their members to UN to make a case for their new regime to be acknowledged. Because of circumstances he actually had a chance to convince them, when Steve Rogers attacked him. Instead of stopping the villain by beating him, the villains got what they wanted - starting Blood on the Debate Floor makes your side look unreasonable and politicians more likely to side with your opponent.
Similiarly said group of supervillains shows up more in his New Avengers run. Their leader Namor gathered them to basically do horrible things for greater good. However when you have dangerous supervillains and criminals doing things, they tend to go overboard. And the fact that Namor has standards makes them incredibly difficult to control, as the villains aren't afraid of him. Instead it just makes them betray him even quicker than usual.
Doctor Faust uses his high grade of magical prowess to make his way through to fight Doc Fate, and prepares himself for a Wizard Duel. Unfortunately for him, that is all he brought to the table, whereas Doc Fate brought his magical prowess, underhanded tactics, and a gun. He manages to hold off the zombies that come at him with the gun, and summarily defeats Faust with a Groin Attack.
Lady Shiva, upon losing her plane, prepares to fight the Blackhawks with her sword, her close combat skills things of legend. Unluckily for her, the Blackhawks have handguns, and prove that bringing a sword may not have been the best idea.
During the first arc of Ms. Marvel (2014), Kamala brags about fighting crime in the classic, "politically incorrect" (her words) costume that Carol Danvers used to wear before she became Captain Marvel. She quickly finds out that despite looking cool, heels are not practical to run or fight in, and that Carol's sexy leotard gives epic wedgies. Carol had Required Secondary Powers like flight that dealt with the impracticality of the costume for her and even than she ended up ditching it after a while. Kamala doesn't have those. She switches to a new, more practical suit a short time later.
In Batman, Mister Freeze's ice-gun was the Trope Codifier of Harmless Freezing in the Silver Age. Post-Crisis however, Freeze has killed plenty of people using it and whenever Batman and company get hit by, the story tends to make a point about how quickly they have to escape; turning somebody into a block of ice is pretty fatal to say the least.
An issue of New Avengers showed a realistic downside of super durability. Luke Cage's incredible durability means that he's extremely hard to injure but also means that if something actually does manage to hurt him, doctors aren't able to operate on him to properly repair internal injuries or even give him a shot; his skin is so strong that scalpels and needles just break when pressed against it. This results in Cage nearly dying from his injuries and spending the next several issues out-of-action as he heals the slow, hard way.