Special mention for "The coming of Galactus" trilogy, 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, he 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.
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?
The Black Panther punched out Mephisto once. With his bare hands. However, it turns out he was backed up by Applied Phlebotinum (as is often the case with these situations.)
And I'm sure a lot of people will remember the time Spider-Man 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. If that isn't pretty damn impressive, then I don't know what is.
Wait, scratch that. Just found something even MORE impressive. Spider-Man has beaten both Thor and Thanos. Not kidding. here◊ and◊ here.◊
Probably gets it from hanging around the Fantastic Four so much.
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.
Whenever Darkseid was confronted in Pre-Crisis... all attempts in punching him out ended in failure. Even when Superboy and Supergirl were amped up by Highfather to insane amounts? The same two who could pull an entire galaxy's worth of planets without said power up? None of their punches even hurtDarkseid and barely even catches his attention.
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."
Legion Abstract: Doesn't sound noble, until you think about it: for Mon, the Time Trapper isn't a person so much as he's a force of entropy; if you kill him, is it murder or experimental physics?
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.)
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.
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!
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 a recent 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.
In Preacher, the protagonist has the nerve to use his Word power on God himself. I'm not kidding. He actually tries to make the Creator of everything do his bidding!
And loses an eye for his trouble. Of course, this overlooks the far more impressive fact that the Saint of Killers started his career by shooting the Devil and ending it by shooting God.
In a one-off Judge Dredd 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.
How has no one mentioned Ash Williams shooting Freddy Krueger in the nuts in Freddy vs Jason vs Ash? He shot Freddy Krueger—who by now had god-like powers—IN THE NUTS!
And not only that, he also rams his car into him before that!
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.....
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 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.