This is the main focus of Campione!, whose titular warriors gain their title when they defy all common sense of the world and successfully kill a Heretic God.
Masaru of Digimon Savers literally punches out a god. As an encore. The punch shatters said god. And that still isn't the most ridiculous of his punches. Throughout the series, Masaru frequently punched giant Digimon and actually harmed them, to the point where he was literally incapable of making Agumon evolve without first punching a Digimon. His father Suguru was shown to do pretty much the same thing in a flashback, and the two are the only human characters to do anything like that.
Masaru returns in the finale of Young Hunters, and his debut involves falling from the sky and punching VenomMyotismon in the face. Notably, he's the only human in the entire group to actually get up and join in the fight (unless you count Takato and Takuya while they're in Digimon form). He and Shoutmon kill two MaloMyotismon with two punches.
Mazinger Z: Done by Kouji Kabuto in the Mazinger-Z vs Devilman movie, when he beats the crap out of an army of demons piloting his Humongous Mecha.
Not quite. Even though they did defeat it, it was only temporarily and it took Reinforce sealing herself away for all eternity to finally put an end to it.
It should be mentioned that they only beat the actually really Cthulhu-esque "Darkness of the Book of Darkness". When Nanoha and Fate fought against Reinforce they didn't stand the slightest chance. She's made to be a powerful being that can destroy entire worlds and she does not disappoint.
Several of the main duelists in Yu-Gi-Oh! are able to (or come close to) take out the legendary Egyptian God Cards with a series of impressive, but otherwise mundane, card combos. Examples include:
Yugi uses Malik's own Osiris infinite combo against him to deck him out.
Joey nearly took down Marik's Winged Dragon of Ra with his Gearfried the Iron Knight, but he fails before he can give the attack order.
He fell into a coma in the English dub while, In the manga and the Japanese anime, he dies and recovers.
During their final duel, little Yugi managed to take down all three of Atem's Egyptian God Cards with a combo involving his Magnet Warriors and Osiris' own effects, a feat that had the distinct honor of forcing the otherwise-stoic Kaiba to acknowledge the little twerp as his better.
Also in the final duel, Yugi manages to simultaneously increase the Silent Swordsman's power while decreasing Obelisk's power so that the two of them manage to destroy each other. Near the end of the duel, he seals away Monster Reborn, and then reveals that he did so when Atem tries to resurrect Osiris, preventing the resurrection and enabling him to directly attack him and win the duel.
In 5D's, Jack Atlas goes up against the Crimson Devil, Scar-Red Nova, the oldest Earthbound God that drove the Crimson Dragon to it's limit. During the battle, he acquires Burning Soul, and robs the Crimson Devil of all of it's power, using it to make his new ace monster.
Furthermore, in Mai-Otome, Arika manages to defeat Nina, who was at the time, powered up by the Harmonium and capable of destruction of apocalyptic proportions, with almost disappointing ease.
In Sailor Moon, Sailor Moon defeats the personification of Chaos itself as well as its four incarnations. Naked, no less, while jumping into a metaphorical Shark Pool.
In The Slayers TRY, Lina and company destroy a fusion of the highest ranked demon and god from another plane, bent on remaking all planes of existence free of strife. Granted, they had access to a prophecy on how to destroy it.
Does slaying Dark Lords (especially one that literally plays with the souls of humans) that have godly levels of power count if you channel the supreme god and creator of your multiverse to do it? Because Lina does this. Twice. And the second time she screws up and is possessed by said creator of the multiverse.
Not really; the first sub-Dark Lord that was defeated was done so by another sub-Lord, and while Lina intended to destroy the second with that spell, she gets possessed before it attacks and the Lord of Nightmares herself kills the lord. There's a third that was fought in the novels, but it barely survived.
At the end of Evolution-R, she just killed the fragment of Shabranigdo she had destroyed in the first season but that got resurrected... again. That's right, Lina has now been personally responsible for the destruction of a one-seventh fragment of the ultimate evil god of her world... twice. Take that, Cthulhu. (Lina actually defeats Shabranigdo twice in the novels as well, although the events surrounding her second victory are very different from those of the anime.)
Kyon nearly punches Haruhi (read: The Omnipotent subconscious Reality Warper with Anti-Social Personality Disorder) when her physical, psychological and sexual abuse of Mikuru goes too far, specifically for getting her drunk, then smacking her on the head repeatedly for not being able to act well because she's drunk. Thankfully, Koizumi is able to physically restrain him, but Haruhi learns regret when she realizes that she finally managed to well and truly piss off Kyon.
At the end of The Disappearance of Haruhi Suzumiya, Kyon domineers over the Data Overmind, which has nearly godlike powers, by threatening to provoke Haruhi into recreating the universe with him, to a place where the Overmind would not exist. Which is in some ways more impressive than just Punching Out Cthulhu. After all how many mortals have ever made a god back down in fear?
In Code Geass R2 episode 21, Lelouch uses his Magical Eye on the "collective unconsciousness", a gigantic mass of souls without physical bodies, which his father Charles says has been referred to in the past as God.
Though the guide states that the people/collective unconsciousness already wanted a tomorrow implying that Charles' plan was doomed from the start. If you rewatch the scene you can clearly see that Lelouch asks it in the form of a request, and even uses please.
And in the manga, Guts is attacked by Slan of the Godhand but manages to fight her off thanks to his Evolving Weapon. It is averted somewhat, as the body Slan was in was only a construct made from what was available (e.g troll guts), and he didn't actually kill her.
Later, Guts manages to wound Emperor Ganishka, an absurdly powerful being made of mist, in an act that not even an army of demons could accomplish, thanks to said Evolving Weapon.
And now, Guts has killed the Sea God, essentially the Berserkerverse's equivalent of Cthulhu.Yep.
Getter Robo punches out (or Getter Beams, or axes, or drills, or...) absurdly powerful baddies every Tuesday, and sometimes on Mondays, Wednesdays, Thursdays, Fridays, Saturdays and Sundays.
In the Kyoto Arc of Mahou Sensei Negima!, the Big Bad was successful in summoning a massive Demon God of 1600 years ago which wasn't even scratched by the best attacks of the main character. It seemed like nothing can stop it now. Then Evangeline appeared and demonstrated just how powerful she was by taking it out with one shot. The scary part is, based on Rakan's Power Level chart, the Demon God was, far, far, far stronger than anything Negi faced even after nearly 200 chapters.
Perhaps subverted because, if all the stories about her are true, Evangeline herself is a Cthulhu. The demon had a fearsome reputation and great power but so did Evangeline.
And then there was Nagi, who, when faced by a being known as the Mage of Beginnings and the Lifemaker that had just wiped out his entire party with one attack, proceeded to take said being out with what looked like a super-powered Shoryuken. Possibly subverted as the Lifemaker wasn't destroyed - it possessed Zect and later Nagi himself.
The Anime version of Soul Eater takes this trope very literally as the series ends with Maka defeating the Kishin, a god-like, nigh-omnipotent being fueled by madness with a single punch, fueled with the power of Courage!
Special mention should go to Black*Star, who in the previous episode managed to beat the fuck out of the Kishin, pretty much on his own for a decent portion of the battle. Maka may have slayed him but Black*Star held his own pretty well.
In Death Note, Light manages to manipulate Rem, a Shinigami into violating a rule for which the punishment is death.
Not to mention, after he becomes the 'God of the New World' i.e. killed L when his god complex reaches its height, he ends up getting shot. By Matsuda.
Eneru from One Piece claims to be a god, as he is made out of pure lightning and no one can touch him. In comes Luffy, who literally punches out Cthulhu because he is made of rubber, which doesn't conduct electricity.
Screw that, Wiper beat Luffy to the punch on that one. A few things of note: Wiper is not made of rubber, he's just as vulnerable as any other human, and his main weapon is the Reject Dial, a weapon that sends attacks back at the enemy while causing potentially lethal impacts to the user. Wiper enters into single combat with Eneru, and using the Reject Dial, Seastone skates, quick thinking, and just plain Bad Assdetermination, actually kills Eneru. Eneru's lighting restarts his heart, but Wiper actually killed him!
Scratchman Apoo dealt a would have been a lethal blow to Admiral Kizaru. If Kizaru wasn't a Logia user, he would have been killed. Kizaru kicked him into a building afterwards, but Apoo still managed to get away.
When Luffy met Whitebeard, the most powerful man alive that could move entire islands with his tsunamis and earthquakes, he automatically challanged his title as King of the Pirates. Almost everyone in earshot were stunned to hear Luffy do this.
In a more literal example, shortly after the Time Skip, Luffy one-shots a Kraken, and later tames it.
Not to mention that this is after he's yelled at Zoro and Sanji for doing too much damage to it before he can punch it. Cutting or kicking Cthulhu just will not do.
All the above examples are nowhere close as epic as this one. While possessing no superhuman feats, the World Nobles are untouchable deities. Any offense made against would immediately ring up the arrival of a Marine Admiral, whose power is of One Piece's equivalent Cthulhu, with the mission of completely terminating the offensive factor. This grants these World Nobles the status of God and the freedom to do WHATEVER they like, including killing for no reason or torturing slaves to death. Well, guess what happened when one of those bastards tried to murder one of Luffy's friends out of pure racism and entertainment. For Anime, enjoy watching Anime turned back into Manga for a few seconds.
This is also the general reaction by those in the know about Luffy's defeat of Crocodile early in the series. A rookie pirate out of East Blue, widely regarded as the weakest ocean, taking down a Warlord of the Sea is huge. His bounty goes up over 300%, launching him to Supernova status after only having landed on four islands in the Grand Line.
In Naruto while the Tailed Beasts are far from "gods" and more obviously related to "great demons", each of them was separated into their own form by the Sage of the Six Paths, who bested and divided their original form as the Ten-Tailed Beast. Then, many generations later, all nine of the Tailed Beasts have been at some point defeated by ancient ninja legends and sealed inside the bodies of their descendants.
Notably, most times when this trope is invoked in the present-day of the storyline, it usually fails. Orochimaru vs 4-Tailed Naruto, Sasuke vs Killer Bee, and Pain vs 8-Tailed Naruto.
This is the signature move of Takashi Natsume from Natsume Yuujinchou. He can deliver a punch that lays out youkai many times larger than him, much to their surprise. It's implied that it's not just physical force — he inherited very strong spirtual power from his Identical Grandmother Reiko Natsume (who delivered most of her beatdowns via baseball bat.)
At the end of Rebuild ofEvangelion 2.0, Shinji and Unit 01 have started Near-Third Impact and are spoken of as things beyond any ever seen. Then Kaworu stops that by dropping a lance on Unit 01 from above. It's revealed in 3.0 however, that Kaworu wasn't able to stop Third Impact as a whole, thus killing off a good chunk of humanity.
The main plot of Edens Bowy revolves around god hunters, humans who have the power to slay gods, and thus protect humanity from divine enslavement.
Saint Seiya enjoys and employs some very literal god-killing, it being the plot is basically 'oh crap, a Holy War, go kill Hades for me (Athena)'. So they do, killing Hypnos and Thanatos along the way-and in the movies they beat up Artemis and Apollo. Also seen in Saint Seiya: The Lost Canvas, where at one point it's four Gods against Capricorn El Cid. with some help from The Hero and a good old Heroic Sacrifice, he wins.
To say nothing about Cancer Manigoldo, who pretty much spends the entirety of the fight against Thanatos hanging on for dear-life as he gets curbstomped further and further into the ground, only to claw back from the brink every time and eventually destroy the God's body.
The grand champ of this all now is Gemini Aspros, who managed to kill a Titan with powers comparable to Chronos single-handedly.
In the manga Shin Angyo Onshiafter Aji Tae has just annihilated everyone in the army who has a pure heart, an unburdened conscience, or who loves somebody by telling them "Die", Munsu walks into the courtyard and punches Aji Tae in the face. It turns out he is immune to Aji Tae's powers.
Almost literally in the second-to-last chapter of Fullmetal Alchemist: Ed punches Father, who has recently absorbed a god, in the face. Hard. Considering the being in question is generally able to alchemically block, disintegrate, or explode anything incoming without moving, this is especially impressive.
Before that, all of the protagonists do this in the final battle to get him to use up his stone. For a while it doesn't seem like anything is affecting Father, as he just stands in one spot using his powers to deflect the attacks. And then something changes and he's actually forced to block an attack with his arm. This doesn't go unnoticed by the heroes; cue orders to hit him harder with Father getting knocked around from all sides.
And before this, Rider, who helps Saber out with Caster's Cthulthu, gives a badass speech to Waver about how his attempt to take over the entire world while he was alive was his big Cthulthu punching moment. He knew from the start he had a slim chance of success, but he did it anyway, because he had the heart of the King of Conquerers.
Rider: Look at this boy, (points to a map of the world) this is the opponent I’m fighting. Now draw a picture of us two, right next to this enemy. And do it to scale, that we may compare ourselves.
Dragon Ball Z has this as a recurring theme when the Big Bad of each arc is defeated by Goku. It is actually invoked by the cast when Future Trunks is introduced and destroys Mecha Freeza, the Big Bad of the previous arc, in mere seconds.
Given that in Pokémon Special it's rather common for bad guys to capture legendary Pokemon to use for nefarious purposes, the good guys have to punch the legendaries out to prevent them from doing major damage.
Ash from the The Electric Tale of Pikachu, in the fourth volume, basically kills a giant, high-level Haunter that the previous inhabitants of the area worshiped as a god. He was actually trying to catch it, but the Haunter had a god complex from all the worship it received and blew itself up rather than get caught.