Batman: The Dark Knight Returns: Bruce Wayne (then retired as Batman) has gone for a walk through Gotham City at night and crosses paths with two Mutants who plan to murder and rob him. They scrap the plan, in part because yes, he's physically intimidating, but also because he's "into it", and "can't do murders when they're into it..."
Batman: No Man's Land: Early on, there were a series of interludes starring a character called "The Punk". His M.O. was trying to steal supplies by threatening people with an empty gun. The twist was that all his intended victims knew that no one had any supplies, including bullets. The last of the stories was titled "The Punk and The Stranger;" it features the title idiot attempting to rob a strange, pale man in a purple raincoatwho seemed inordinately happy with everything. No points for guessing why this was the last "Punk" story.
When Bruce Wayne was arrested during the Bruce Wayne: Fugitive arc, some skinheads decided to teach him a lesson. In a pitch black cell. It ends about as well as could be expected. Though it doesn't help his case as the lawyers try to portray it as Bruce beat these guys up for no reason and as proof he was a killer.
Batwoman: During Kate Kane's aimless period of alcohol abuse, she's on the phone with her ex-girlfriend outside a bar when a mugger armed with a pipe tries to take her for an easy mark. Unfortunately for the thug, Kate was fairly recently a top cadet and boxing champion at West Point, with all the unarmed combat training that implies, and is in an extremely foul mood to boot. Kate promptly beats the crap out of him, pointing out that he thought she was just a victim, but that she is a soldier. She is only prevented from really messing the guy up by the timely intervention of Batman, who had presumably intended to sweep in to save the socialite from the thug, only to find himself doing the opposite instead. With the fight essentially over, all that Batman can do is extend his hand to Kate before leaving to answer the Bat Signal.
Robin (1993): Three jerks attack Tim Drake outside a movie theater and he can't really fight back because he is with his girlfriend so he focuses on limiting the damage they do while not looking competent. Later they spot him while he's on his own and he intentionally takes a "short cut" through an alley with no witnesses. This time when they go to attack him they're all left moaning and bleeding, and Tim walks away with a spring in his step.
In Batman: Gotham Knights, Batman, Batgirl (Cassandra Cain), and Robin (Tim Drake) are shot down in the Bat-Plane by Kobra goons. Batgirl then uses a Wounded Gazelle Gambit to lure out the attacker, claiming the others were killed in the crash. When the goon grabs her and says that he won't show mercy, she simply responds that she will treat him in kind, and beats the crap out of him.
In the first issue of Batgirl (2009), three small-time crooks spot a redheaded woman in a wheelchair riding the subway alone and try to mug her. What follows is a black panel with several screams, followed by an entirely-unruffled Barbara Gordon getting off the train.
In a twist in Batman: Black and White #3 (2013), when a serial child-napper chases his latest victim into a dark alley, they interrupt two women about to break into a bank — one wearing a jester costume and the other wearing an outfit made of foliage. The little girl assumes from the costumes that they're superheroes and pleads for help, the pair place themselves between her and the kidnapper, so he tries to knife them. They give him an instant curb stomping.
The Supergirl-Batgirl Plot: As Batmite is posing as Batgirl, a crook waves a gun at "her". Of course, a firearm wouldn't frighten Batgirl, let alone a reality warper extra-dimensional imp.
Birds of Prey: Many are the unfortunate (now dead) bikers who thought Lady Shiva would be an easy target.
Darkseid got mugged once when he visited Earth in disguise. He didn't really do anything to resist and just analyzed the whole experience, finding it rather interesting to be on the receiving end of this kind of behaviour for a change.
In Doomsday Clock, we see the second Rorschach definitely follows his predecessor’s footsteps in regards to this trope. One unlucky supervillain in Arkham mistakes him for a normal criminal and picks a fight. The next thing we see is Rorschach being dragged to a cell, covered in blood and with a chunk of flesh in his mouth.
In The Button, the prelude to Doomsday Clock, Eobard Thawne the Reverse-Flash is certain the Speed Force makes him invincible or will enable him to escape when he goes after the one affecting the Multiverse. He instantly learns how fatally wrong he is when he meets Doctor Manhattan.
Green Lantern Corps: In the 2011 series, a series of events results in Guy Gardner losing his power ring and landing in jail on Earth, where he's sexually harassed by his cellmate. The cellmate thinks Guy will be a pushover without his ring. Guy manages to beat the snot out of him without even looking in his direction.
Parodied in the Harley Quinn and her Gang of Harleys miniseries, where one of Harley Sinn's Psycho for Hire minions comes across a group of homeless people in an alley and pretends to think that they're going to attack him so that he can kill them for fun. Harlem Quinn turns up and rescues them.
JLA (1997): In one issue, Lex Luthor, highly successful billionaire business tycoon, launches a plan to cripple the JLA using non-criminal techniques from the business world. Unfortunately for Lex, he's completely ignorant that one of his adversaries is really Bruce Wayne, a highly successful billionaire business tycoon in his own right (and one who does it as a sideline). The art highlights this, showing Batman sitting at the computer with his cowl down, making it quite clear which persona is fighting this battle.
Mister Miracle:
In a issue, a mook tries to kidnap Big Barda in order to force Scott Free (Mr. Miracle's alter ego) to sign an insurance policy for his Mob Boss. After his wife tells him what happened, Scott asks her if the mook is OK. The mook is OK, but very afraid of the possibility of seeing Barda again.
In a crossover with Superman (in his book), Mister Miracle goes missing while trying to help the titular character. Barda goes to look for her husband and her search leads her under the sea. There, a shark tries to bite Barda's butt. She sends the shark flying.
Deadshot and Catman are discussing the potential Heel–Face Turn that Catman underwent in Africa when they enter a convenience store that is in the process of being robbed. They completely ignore the brandished weapons and pick up some cigarettes and ice-cream and even go to pay for their items, all the while being screamed at by the skinheads who are doing the robbing. After a little while, Deadshot takes a break from the conversation to easily disarm the skinhead behind him and then berates him for his amateurishness. As he explains, it is fine if the skinhead does not respect him, but he will damn well respect the gun. Deadshot gives the thug a few pointers (start the robbery by placing the gun against the victims head in order to give him a primal fear reaction, but then speak slowly and calmly in order to keep anybody from panicking and reacting, etc.) and then shoves his head through a glass case, taking out one of his eyes, as punishment. Of course, Deadshot then finishes the robbery, taking the cash from the register, to punish the store for "lax security precautions." After Catman and Deadshot leave they resume their previous conversation, but Deadshot immediately points out that Catman, despite what he may think, has not become a good guy. When Catman asks why, Deadshot points out that he just left several defenseless witnesses in the same room as a group of bloody and angry thugs who will be looking for vengeance and to cover their tracks after their humiliating fiasco of a robbery. Catman pauses for a moment, sighs, and walks back into the store.
At another point in the series, a particularly stupid mercenary decides it would be a good idea to try to rape Cheshire. Cheshire, who is considered the second most deadly assassin on the planet. Cheshire, who is internationally infamous for committing genocide For the Evulz. And heknewwho she was! Needless to say, when she starts chowing down on his face, it's impossible to feel any sympathy.
Shazam!: A guy groped Mary Marvel, and it took Supergirl to stop her from tearing him limb from limb.
In The Supergirl from Krypton (2004), a naked Kara wanders confused into an alley, having just woken up from her rocket, and is spotted by three workers. One of them mistakes her for a prostitute and decides to play Lothario only to have his hand crushed and be slammed through a wall. The second tries to help his friend. The third wisely proclaims he's not with the other two and offers her his coat.
In Supergirl (1982) issue #19, two crooks stalking a park at night spot a woman sitting alone on a bench. They approach her from behind and bludgeon her with a pipe... which gets bent. Then they notice her Supergirl costume... and her pissed off expression.
Supergirl: I take it this [pipe] is yours, guys? Crook 1: H-Holy...! It... It's... Oh, man, it sure is! Hey... We're awfully sorry, lady... Honest! We didn't know it was you! Supergirl: I'm kind of glad it was! My head's made to take this kind of abuse!— Is yours? Crook 1: Oh... Momma... Crook 2: P-Please... Don't do it!
In Supergirl: Cosmic Adventures in the 8th Grade, the Stanhope School students spend weeks mocking and bullying the new transfer student, Linda Lee (who happens to be the Girl of Steel).
Superman had gone into a dark alley and a guy jumped on him ("Hmmph! What are you, a bodybuilder or something?"). Guy gets thrown into the sacks of garbage, tries shooting at the shadowy figure, and then nearly pees his pants when the bullets bounce off the big red "S" and a big Kryptonian fist starts hurtling towards his face. Fortunately for him the fist was catching a ricochet.
In Who Took the Super out of Superman?, Steve Lombard bullies Clark Kent right after Clark has decided to drop his "mild-mannered pushover" act for one week, and gets quickly knocked to the floor.
In Superman: Brainiac, Lombard bullies Clark several times. Clark tolerates his antics until Steve makes a pass at Lois Lane, fully knowing they're married, and stealthily -and literally- knocks Steve on his butt.
In Last Daughter of Krypton, Simon Tycho sends his private troops to retrieve a space rocket which has crashed in Siberia. When they arrive at the place and come upon a girl stumbling dazedly out of the pod, they attempt to capture her. The black ops squad barely have time to catch a glimpse of her S-shield before she throws all of them away.
In Supergirl: Woman of Tomorrow, a nameless mercenary is making off with a little girl's sword when an unknown woman grabs the weapon and tells him to go away. The bounty hunter attacks her, and he finds out two things: her body is too tough to be pierced or sliced by his sword; and she is strong enough to easily take him out.
In The Strange Revenge of Lena Luthor, soap-opera scriptwriter Greg Gilbert is bringing Linda Danvers to his apartment when they are ambushed by a mobster's enforcer, unaware that Linda can obliterate him in a fraction of a second.
In The Phantom Zone, a Metropolis Police SWAT team tries to arrest Az-Rel and Nadira, unaware that they are Kryptonians, and are quickly killed off.
The Plague of the Antibiotic Man: When he sees Clark Kent holding a glass of water as speaking to a woman, Steve Lombard slaps his back so Clark's glass splashes the woman. Later, Superman pays Steve back by blowing Steve's water on the same woman's face, and he wonders what Steve's reaction would be if he found out who he is picking on.
Superman:"I probably shouldn't have done that... But after what that jock did to me on the train, I just couldn't resist! Poor Lombard! If he only knew who he was ticking off every time he picked on meek Clark Kent—!"
Supergirl (1984): When Linda Lee begins attending Midvale High School, two bullies called Myra and Muffy try to play nasty pranks on the newest student. Given that she is secretly Superman's cousin, every prank fails resoundingly, often backfiring on them.
The Death of Luthor: A squad of robot soldiers see Supergirl flying out of the frozen planet which they are watching over, and unaware of her power, fire at her. Two panels later their broken bodies are scattered all over their ship's floor.
"The Super Dog from Krypton": A couple of crooks steal from Jonathan Kent's general store right in front of the owner's son, unaware that he is Superboy. While making their getaway, they shoot a stray dog -Krypto- who was passing by, and are shocked when the growling pooch just ignores their bullets.
"Superman and Spider-Man": Steve Lombard keeps wearing down the patience of Clark Kent and later Peter Parker's with his bullying and pranks, blissfully unaware that either of them could snap him in half.
In Superman/Masters of the Universe crossover "From Eternia— With Death!", a brawler called Crusher tries to start a bar fight with Adam, believing him to be a pampered princeling, ergo easy pickings for a bully. Their fight is ended when Teela and three royal soldiers show up and tell him "Go away or get shot", but should the brawl have continued, Crusher would have learned that, even when he is not transformed into the powerful He-Man, Adam still has super strength.
In an issue of Power Girl (2009), a pervert gropes a very tall and busty blonde in a subway. Bad idea...
While Dr. Manhattan is giving the interview, Laurie and Daniel fight off a group of muggers. Not a word of dialogue is written for this event, and instead it is overlaid with the aforementioned interview.
A flashback to a bit of Rorschach's back story also involved this: the two older boys who accosted little Walter had just been about to "pants" him when he swiped the cigarette one of them was smoking and jammed the lit end into his eye. Then, while the first boy was screaming, Walter launched himself into the terrified other bully and started savagely chewing on his face. In addition to having been a major turning point in his life, this incident makes a neat Call-Forward to the grown-up Rorschach's methods as a highly unpredictable Improbable Weapon User in the rest of the series. Also to the fact that he often gets blamed for brutally attacking enemies in self-defense that others don't know about and never clearing up his name.
Wonder Woman (1942): The fact that Etta Candy regularly fights supervillains, invading aliens and Nazi spies is not publicized so when a trio of gangsters think she's overheard them plotting Insurance Fraud in "Etta Candy and Her Holliday Girls: The Toothache" they decide to attempt to kidnap and off her. This does not work out well for them and when she hands them over to the police they've all been beaten unconscious.
In an early issue of Hellblazer, a bunch of racist skinheads get ready to beat up a hunched-over bald guy in a trenchcoat, thinking he was a homosexual. He turned out to be the demon Nergal, the first real Big Bad of the series. He brutally dismembers them before turning their remains into a singular monster, enslaved to his will.
Lampshaded in an early issue of The Invisibles, when a gang of homophobic rednecks are about to assault the group:
King Mob: I'm telling you that you're in the wrong film, fatboy. You're not in the cowboy film you thought you were in. This is a different kind of movie. And you're in the scene where the redneck shitkicker picks on the stranger in town, only it turns out to be big Arnie or a gang of vampires. I'll bet you've seen that a million times, cowboy.
In Garth Ennis's Preacher, Sheriff Root and his squad of heavily armed men, backed up by a helicopter, threaten the Saint of Killers, an invincible, immortal, merciless killing machine with a pair of revolvers that never run dry, never miss, and always kill. Needless to say, it ends badly for them.
A couple of unfortunate criminals try to mug the Corinthian. Oh, shit. Whoops. It would be a great establishing scene for what his character is like, if his very first scene had not been so... memorable. (It helps that they mistook his sexual interest in young men as a good reason to target him, when it's really a very good reason to avoid him.)
Nor is it a good idea to try to steal a large ruby from a certain tall pale stranger: the King of Dreams might decide to haunt your every night with dreams of the gallows until death comes as a relief.
In "The Hunt", Vasily stays at an Inn of No Return where the innkeeper murders guests for their valuables. Since Vasily slept on the floor instead of the bed, the innkeeper's surprise attack fails. Since Vasily is a werewolf, it doesn't end well for the innkeeper, and it's heavily implied that Vasily ate him.
