Let us not forget the time that one of the The Flash Rogues (Who are considered useless in their own right) called "The Trickster" (a former aerialist with no superpowers, and who uses rubber chickens and yo-yo's to fight) tricked Neron (AKA Satan) into letting him out of hell.
Special mention for "The Coming of Galactus", by Stan Lee and Jack Kirby. It was basically the first time this trope came into play in superhero comics. Nowadays, Galactus is a standard character, we have seen him defeated or humbled several times, we have seen characters even more powerful than him many times, we have seen superheroes fighting hopelessly against such ultimate forces basically once a year or more, we are used to them coming on top of all that as if it was nothing... but by then, when Lee and Kirby wrote that story, nothing of that applied. The Fantastic Four were facing a foe of such power that was completely beyond anything else ever seen before in either Marvel or DC.
Allegedly, the inspiration for Galactus comes from Lee and Kirby brainstorming what to do for the 50th issue, when Lee asked "What if they fight God?"
One of the Ghost Rider characters has an ability called Penance Stare, which forces people to experience the suffering they have wrought on others. In one Fantastic Four cartoon, he uses this power against Galactus. This trope applies to every time that Galactus has the misfortune of ending up in a Super Hero comic, so you know he's going to lose anyway, but this example may take the cake. Later Riders also gained this power. But in this instance, the Rider was merged with a kid named Danny Ketch, and was a half-angel, half Demon who was actually the Angel of Death at the time of this show. He was originally human and named Noble Kale. Head exploding at the strangeness of this character's plot probably ensued on a massive scale when this all came out.
Heck, he's even fought Lucifer (not Mephisto, Lucifer) and won.
The Noble Kale version of Ghost Rider also killed Blackheart, the son of Mephisto. Given how Mephisto and Satan have been swapped around as though they were the same guy in Marvel for decades, this basically means we should be asking Did You Just Kill Cthulhu? Or more accurately, did you just slaughter the ANTI-CHRIST?
Spider-Man once took down one of Galactus' former heralds, Firelord (also one of his most powerful heralds ever). Without getting hit even once. Firelord got so angry he swore he would kill Spider-Man with his bare hands. Guess what. He failed. Miserably. Only reason he was gonna use his bare hands at all was because Spidey destroyed his Firestaff. Although, technically this wouldn't be considered punching out Cthulhu, but rather "Did You Just Punch Out Cthulhu's Right Hand Man", which is a pretty big accomplishment in itself. This is an alien with so much raw power that he could conquer worlds and destroy planets with the slightest effort, a man chosen by Galactus (freaking GALACTUS) to be his herald. And he's defeated by a human in a spandex spider-suit.
Spider-Man has also beaten both Thor and Thanos. Not kidding. here◊ and◊ here.◊
And more or less literally in the first four pages of The Authority: Prime, a miniseries of, admittedly, debatable quality.
Hawksmoor: What the hell is that thing?
Doctor: Your basic elder god, returned from a dimension it was banished to millennia ago, here to turn Earth into its own personal slaughterhouse.
Hawksmoor: So we're talking...
Doctor: Two minutes.
Every superhero in the DC Universe has punched out the Evil New GodDarkseid, the ruler of Apokolips including nonpowered Badass Normals such as Batman and Green Arrow. This probably explains why Darkseid hates Earth and its heroes, given that his superiority complex makes him believe that he should be able to beat them. He also hates Superman with particularly obsessive hatred, possibly because Superman, whose personality is the exact opposite of Darkseid's beliefs in every possible way, manages to humiliate him again and again.
Darkseid isn't quite in the Cosmic Horror Story category though, and it is often hinted at that Darkseid isn't really trying or isn't at full power when he is fighting the Superheroes. When you consider the ease in which he takes over the world in Final Crisis, this gives those old theories some credence.
Or just says something about the Anti-Life Equation, which he's been searching for for at least 30 years of comic continuity. He was easily defeated time and again without this weapon, and takes over the world in a fingersnap once he has it. Guess that's why he wanted it so bad. Edit: He's never been beaten without plot devices or extenuating circumstances. And most of his past defeats were shown to be avatars. Not to mention the revelation of the New Gods and how much boom tubes scale them down. Or that they represent abstract concepts. Now Darkseid's death in Final Crisis? That's punching out Cthulhu.
Darkseid has a history of keeping worthy opponents alive if they've put up a good fight. This isn't Bond Villain Stupidity as it sounds, considering his "defeats" tend to be more that the opposition's just capable enough that the current plan's no longer worth the effort, and Darkseid has had no few occasions where he converts heroes into his footsoldiers. The trouble of when he brainwashedSupergirl and when his underlings tried to use Batman as a soldier template can attest to that.
The Martian Manhunter explained how things work in the DC Universe in New Maps of Hell when they discovered the "god" they were fighting (who'd ravaged Mars in the distant past) was merely a highly advanced artificial intelligence with, well, a god complex.
"We're the Justice League. We've beaten up real gods and made them cry. You are nothing to us."
Another DCU example is the Titans versus Trigon. Big, unspeakable, demon lord. Has multitudes of worlds bowing to him in abject fear. Yet, in their first outing a group of "mere" sidekicks and new characters, none of which were old enough to legally buy booze, take him down. A couple years later, they do it again.
Runaways: Technically, they only have to survive long enough for the Gibborim's time on this world to run out and wait for the baddies to fade away, but given that the fight involves Molly throwing Victor at one's face, it still qualifies.
The Goon and Hellboy are both pretty much based on this trope. In the latter, while many of the supporting characters often use more traditional methods of dealing with monsters, the main character's usual approach is to punch them really hard with his giant stone hand and shoot them with his Hand Cannon. This is Lampshaded in the Goon/Hellboy crossover issue found in the Heaps of Ruination trade paperback. When confronted with the Communist Airborne Mollusk Militia, and specifically their champion, a massive octopus with a hot-air balloon strapped to his head, this bit of dialogue ensues:
Hellboy: Stand back! I do this for a living!" Goon: Oh yeah? When I come across somethin' like this I just try ta punch it in the head — what do you do?" Hellboy: Pretty much the same thing. The two heavyset heroes go on to do just that.
Captain Atom beat up Nekron, one of three Anthropomorphic Personifications of death itself. Of course, the whole reason Nekron is fighting him in the first place is that Captain Atom's power comes from the life energy of the universe. (So when Cap later beats up another personification of death, the Black Racer, it's a little anticlimactic, frankly.)
As long as they are off-panel anyway. (Except in Doctor Doom's case; that one happened in plain sight.)
Rex Libris has this sort of thing as part of his job. As a public librarian. He even calls Nyarlathotep a wuss.
In the 1970s, veteran scribes Marv Wolfman and Len Wein wrote Incredible Hulk: Stalker From the Stars, wherein the Hulk crosses paths with an Eldritch Abomination attempting to escape its prison beneath the Earth so it could conquer and enslave humanity. In this case, the Hulk doesn't punch Cthulhu out so much as rip him to pieces and burn him alive. Ouch.
Hulk often invokes this trope, whether he's smacking around Thor and Hercules, or smashing some multiversal threat with the Defenders. One early foe of his was the Galaxy Master, whose most common form was a huge gaping maw hanging in the middle of space. Hulk's answer? Jump inside it and smash it from within.
In the current Hulk book, Red Hulk punched The Watcher, then went on to punch an Elder of the Universe to death. Arguably justified in that Red Hulk's energy-absorbing powers basically mean that the stronger his opponent is, the stronger he is.
Wein also gave us The Lurker in Tunnel 13, a Swamp Thing story featuring M'Nagalah the All-Consuming, the shoggoth-like father of life on Earth and fountain of all human knowledge. Swamp Thing causes a cave-in at the mineshaft where M'Nagalah is awaiting the proper alignment of the cosmos that will allow him to conquer the universe, destroying him in the process (at least temporarily, anyway.)
Sláine (Mac Roth) from 2000 AD does this more than once. Admittedly, the biggest Eldritch Abomination that he faced, the High Cythron Grimnismal, was just finishing off his regeneration when Slainé and his party arrived, and could be brought down by the cutting of a few feeding tubes.
Circuit Breaker, in the classic Transformers Generation 1 comics, was able to cause the universe-ending god, Unicron, to scream in pain by attacking him with cybernetic implants she made herself. Granted, she was left catatonic afterward, but still...
The Wretch, a little-known superhero, uses Satan's Literal Genie status against him and, using a birthday card, turns Satan into a crayon. Which he puts into a packet, which contains Beelzebub, Bhaal and Lucifer crayons as well.
In Dojon, Herbert kills the Absolute Evil with just two fingers. Of course he can do it with anyone who's green.
In Green Arrow, back while Hal Jordan was the Spectre, Oliver met his friend after coming back from the dead. He was stunned and Hal shrunk to normal size to approach him. That's when Green Arrow punched Spectre.
Atomic Robo volume 3 has Robo facing down an Eldritch Abomination from outside the universe multiple times across the 20th century, with the help of cars, lightning guns, and Carl Sagan. Existing outside space and time, it keeps coming back, but ultimately all the Robos from each Cthulhu encounter team up for a cross-time beatdown.
In Sonic Universe #4, Shadow, Rouge, and Omega travel to the Special Zone and challenge Feist for his Chaos Emerald. When they fail (for the second time in two days) he taunts them, and invites them back tomorrow because they amuse him. Omega responds by pumping him full of every round of ammo he has. It doesn't kill him, but it does stun him long enough for the trio to grab the emerald and teleport out of there.
It seems to be a common occurrence in Sonic Universe. Four issues later, Sonia and Manik did this to Perfect Tikhaos.
And again in Sonic Universe 25-28, where Silver the Hedgehog struggles against Dark Enerjak. Dark Enerjak can't be beaten, and everything doesn't even scratch him. He defeated all the heroes and villains alike of his universe, leaving only a few around for entertainment value, and has left only Silver and his own daughter, Lara-Su, to oppose him. Besides summoning armies made from all the souls he's taken and hitting Silver with Angel Island, he has a wide array of Chaos powers to add to his invulnerability. Silver eventually realizes that, indeed, he can't stop Enerjak - nobody, not even Super Sonic or Shadow's powers could. So, he uses his own powers to capture Enerjak's attacks and reflect them back at him. Enerjak, arrogant as ever, keeps falling for the trap, until he's so injured he tries to attack Silver physically... only to be defeated by a last, final blow from Lara-Su.
Later on, Krona uses the Cosmic Cube to kill Galactus. And then converts his corpse into a house.
Hawkeye does this to Krona himself thanks to one of his trusty arrows.
Hawkeye: Last arrow I had, TNT arrow.
The Batman does this to Metron, one of the New Gods. He tells Metron that he knows more than him because of his human form. Metron shapeshifts to a Human and says "What's so special about THIS?". Batman punches him. Pow!
Earth's 1's Supergirl lays an absolute beatdown on the Anti-Monitor before being taken out by a lucky shot... and as he limped off the battlefield, the Anti-Monitor said she nearly killed him. That's right, she nearly killed a being who ate universes.
During a fight with Superman, Arion turned into the titular entity. He still lost. So the Man of Tomorrow literally did punch out Cthulhu.
Wonder Woman finally killed Ares the God of War in one arc. She didn't just "beat" him or "banish" him — she killed him. By smashing in his skull with a battleaxe. Of course, Ares isn't completely out of the story yet. Even gods have a hell after all.
In The Dark Tower: The Long Road Home, Sheemie manages to knock down the Crimson King, who is - for all intents and purposes - the universal personification of evil in every single conceivable form of existence.
When Judge Dredd is confronted by the incarnation of Fear itself, the latter attempts to use his Nightmare Face that causes instant death to any mortal on him. Except Joe drokkin' Dredd is no mere mortal. Gaze into the fist of Dredd!
In a one-off story of dubious canonicity, Satan comes to Mega-City One to try and tempt Dredd. Dredd responds by not only refusing his offer, but by beating up Satan, arresting him for the crime of instigating every other crime, and locking him in iso-block 666.
Played for comedy in Damage Control when Edifice Rex (a cosmically-powered crewman) decides to use his powers to reverse the Big Bang and force everything back into the cosmic egg. While an assortment of cosmic beings consider how to stop this, his boss simply fires him.
Of course there was also the time when Batman - Bruce Wayne had just returned from the dead and approached then-current Batgirl and ex-Robin Stephanie Brown. The Bitchslap she gave him was extremely enjoyable and totally deserved - and Batman is a God in his own rights.....
Batman has even, in one of the earliest inter-company Marvel/DC crossovers, taken down the Hulk. That's right, Batman once brought down the Hulk!
In the first Secret Wars, the Beyonder (a being "from beyond", with absolute power) takes a number of heroes and villains and makes them fight among themselves. However, Dr. Doom does not play the Beyonder's game, and arranges things so he can attack and defeat the Beyonder himself, claiming his power.
In Blackest Night, Heat Wave (who's just a guy with a really good flamethrower) manages to pump out enough fire to melt Black Lantern Rainbow Raider's power ring, destroying him. This is notable because power rings are normally indestructible. Heat Wave quips, "Everything has a melting point."
Who could forget that moment in 52 when Black Adamkilled death? (To be fair, it was really a genetic-plague science experiment created by a cult, but still.) Dr. Cale probably summed it up best:
Dr. Cale: Black Adam killed Death, the pale horseman! What does that make him?
There was that time Captain America kicked the Devil's ass, actually defeating the Lord of Darkness in a straight fight. The proof is here.
Big BadDarkhell from Les Légendaires did this in his backstory. Before the Legendaries form to oppose him, he had to face the rivalry of Skroa the Cunning, a Demonical bird sorcerer. Not only did he defeat him, but he also trapped him inside his castle as a test subject and eventually de-powered him by turning him into a regular bird.
In the Smallville season 11 comics, Superman is strong enough to make Hades bleed with a punch. He eventually defeats the god by grabbing him and threatening to throw him into outer space, where he would tumble through the void helplessly, forever. Hades becomes so terrified of suffering such a fate that he surrenders and returns to the underworld.
Lex Luthor has made a career out of trying to punch out Cthulhu, in the form of the Big Blue Boyscout himself. In Last Son he finally gets the chance to kill a Kryptonian, killing one of Zod's henchmen in a one-on-one confrontation.
The Mighty Avengers once defeated Shuma Gorath, one of the most powerful and evil beings in existence. To be fair, there were a few things in their favor: the thing they defeated was a mere fragment that was trying to establish a beachhead to bring in the rest of it, and they defeated it by empowering and invoking another deity.
Xadhoom, a Physical Goddess if there is one, is practically a living star in a humanoid form. She absolutely hates the Evronians, who destroyed her homeworld. Physically, Evronian warriors are on par with humans, and their weapons cannot even scratch Xadhoom, not even the starship-grade ones, while Xadhoom can annihilate their ships without effort. And yet, the Evronians defeated her twice, and nearly got her twice again:
her first defeat was in the very issue she debuted in style, when a group of warriors dismantled their ship's engine to put together a forcefield capable of resisting everything she could use except that one attack that would have killed her and destroyed Earth. Had not they been forced to use the local power plant to power it (meaning One could just shut it down), Xadhoom would have been defeated then and there;
the first near defeat was when they attacked her with a weapon capable of absorbing even the power of a star. That was working... But not nearly fast enough to prevent her from retaliating;
when Xadhoom went to destroy their mobile worldship, the defense fleet had an improved version of the forcefield projector mounted on one of their ships. They snuck up on her, fired... And Xadhoom, having noticed them trying to hide from her, dodged and had them hit another of their ships, before disintegrating both;
after Xadhoom routed the defense fleet, they pulled out something she could not destroy: the survivors of her people. They forced her to surrender, and realized how they could kill her and were about to do just that when Paperinik freed the survivors... At which point Xadhoom promptly broke out and started exterminating the Evronians.
Moldrock may be less powerful than Xadhoom, but is a Physical God himself with enough firepower to conquer a planet by himself-and he proves it when he attacks Duckburg and casually defeats the US troops trying to stop him while being weakened. We first meet him while he's stuck in Everett Ducklair's Pentadimensional World, a prison dimension that drains his powers (hence why he was weak when he conquered Duckburg: he had not yet fully recharged his powers after escaping his prison), with Everett having defeated him with a weapon that literally stopped his subjective time and then put a suppressor crown on his head.
Dungeon Twilight: Herbert One-Hit Kill Absolute Evil thanks to his skin turning green making him vulnerable to Herbert's Finger Poke of Doom. Soldiers all around renew allegiance to him after seeing him kill the gargantuan beast in such fashion. His son Elyacin was on his way to do it with strength alone.
The Súper at the end of "El bacilón". OK, you have an urgent necessity to go to the bathroom, but the unstoppableMuck Monster that has been terrorizing the city for the last week is obstructing your way. What do you do? If you're the Súper, deliver a SINGLE slap so that it dissolves into nothing and stops obstructing your way. No more Bacilón. But, unfortunately, this does little to help him relieve himself.
In "La máquina del cambiazo" ("The swapping machine"), Mortadelo is warped into a creepy old castle through the titular swapping machine, and a bat enters the TIA offices instead. Filemón tries to catch the bat so they can swap it back with Mortadelo, when the bat suddenly turns into a very menacing (for the comic standards) Count Dracula. Unfazed, Filemón delivers a single slap to his face, leaving the vampire groggy, and drags him by an arm mumbling: "Yeah, such a moment for counts to show up... Come on!", before kicking the Count back to the machine.
Surprisingly, even Galactus has done this. After getting a new purpose and a power boost thanks to the Ultimates, he successfully defeated Master Order and Lord Chaos. Bonus points for literally (well, sort of) punching Master Order in the process.
The Tales of Cthulhu short story "Alimentary, My Dear Cthulhu" is a detective story pastiche where the victim is one of the Great Old Ones, killed in the library with the candlestick. Out of sexual jealousy.
She once ate several eldritch horrors in the pages of Justice League Elite while stranded in the Shadowlands.
In addition, her defeat of Lady Shiva was considered this by many. Though Shiva (probably) isn't an Eldritch Abomination, she is treated with a certain reverence as if she were the harbinger of death itself, and had never before been defeated in a fair fight.
Nova: At the end of volume 7, with a little help from Sam Alexander, Richard Rider tears an Eldritch Abomination out of himself.