Shin Megami Tensei has you continuously kicking the crap out of major deities. Best example is the Neutral Path of Shin Megami Tensei II, which ends with you having killed the likes of countless gods, spirits and demons, including but not limited to three of the Four Archangels, Lucifer, Satan, the freaking titanic dragon Kuzuryu, three of God's Names (Shaddai, Elohim, and Sabaoth), ending with having a very serious chat with the old man himself. Other games allow you to challenge Nyarlathotep, Nyx, Izanami, the Riders of the Apocalypse and company, and much, much more; all in all, there is a very sizable stable of spirits baying out for your blood. And guess whose job it is to demonstrate why the power of Humanity is so coveted in these games?
The final boss of that game is YHVH. Yahveh. Yehovah. GOD. And you team up with either Satan or Lucifer (yes, they're seperate beings) to kill him. In the neutral path, neither joins you.
Persona 2 In which the last boss literally IS Nyarlathotep himself, and while he wins in Tsumi/Innocent Sin, in Batsu/Eternal Punishment he loses and you literally Slice, Shoot, and of course PUNCH the ever loving crap out of him before he is forced to retreat.
Persona 4takes this trope more literally than Persona 3 does - the protagonist literally kills Izanami, one of the Japanese gods of creation, single-handedly (Izanami herself says before dying "Power enough to erase my existence...").
He doesn't really do it single-handedly, he does it by summoning Izanagi-no-Okami, Izanami's husband, which is the manifestation of his own psyche.
Nocturne plays with this in its bonus ending. The final boss is Lucifer — yeah, that Lucifer. But he isn't going all out on you, he is just testing if you are good enough. Because once you've 'defeated' him and showed your potential, you become his Dragon and lead The Legions of Hell in a battle against God. That means he probably had to set the bar pretty high... Played even further with the final boss, Kagutsuchi. I mean, (he appears on EVERY route) is literally the embodiment of God's will, the overseer of creation and the new world, and by killing instead of just defeating him, you can end both time and the entire process of creation.
The Four Archangels, Ancient of Days and Sanat Kumara DLC fights in Shin Megami Tensei IV. And even beyond the four greatest archangels in Creation, one of God Almighty's avatars and one of the oldest and most powerful demons, Masakado's Shadow is even worse news than them all. Not even that stops you from being able to halt all of their plans and rampages.
Several cases in Mardek RPG. The Security Demon seems like it is supposed to be an unwinnable battle that you are supposed to avoid but it can be beaten. So far two of the GDM not counting Rohoph, although they are probably the weakest two in a straight up fight, and both the body and soul of something called the annihilator which is stated to have destroyed an ancient civilization.
In Utawarerumono, this trope is given a unique twist: The deity the people in universe worship is both God and Cthulhu, and he asks his own followers to beat the crap out of him, who happens to resemble the Eva Unit-01 crossed with Godzilla. They succeed in beating their own God to the point the Cthulhu half is destroyed forever, just like said God asked for.
In Ultimate Ghosts N Goblins, the True Final Boss is Hades whom Arthur destroys simply by tossing weapons at him until he explodes and takes all of Hell with him.
This sort of thing happens all the time in the Makaimura series. Arthur's beaten the crap out of Astaroth, Lucifer, Loki, Beezlebub, Samael, and Satan.
In Baldur's Gate II: Throne of Bhaal, the final battle pits the epic-level protagonist and his party against Amellisan, traitorous priestess of Bhaal, charged up with about 99% of Bhaal's power. Your protagonist has the remaining 1%. You win.
Happens for both the protagonist and antagonist in the first BloodRayne as both Rayne and Jurgen Wulf can do significant damage to Belial before time runs out and he gains convenient plot-armour with which to smush the both of you. If you find a place to hide so that Jurgen ignores you and focuses almost solely on Belial (he'll still come across you every now and then while gathering weapons), he'll nearly beat him before the time expires, at least 70% on the hardest difficulty IIRC. Since for some reason blades do more damage than guns, as usual, Jurgen will eventually fail in this battle without your help, despite the fact he moves too fast to take damage from the clumsy devil.
You can quite literally do this in Borderlands by playing as Brick.
Call of Cthulhu: Dark Corners of the Earth tries to maintain the bleak, hopeless atmosphere of the Mythos, and the player spends much of the game either unarmed or with insufficient ammo, forced to run away from the monsters trying to kill him. However, at the end, the main character ends up fighting and knocking out Dagon (the 100-foot tall Deep One god) with a battleship's main cannon. When examining a statue of Dagon later on, he even cockily remarks "It's a statue of Dagon, minus the missile I lodged in his face". He later goes on to kill a pair of Flying Polyps with an alien BFG and knock out Mother Hydra herself. And before that, he had single handedly taken out a no less a creature than a Shoggoth (with a little help from some tons of explosive gas in enclosed space). So it's kind of jarring that, after such a string of incredible victories, and finding out he's half super-being he decides to kill himself because of his alien heritage, which he just can't come in terms with at the end of the game.
Also, it's more than unclear if the things you killed/wounded actually were Dagon and Hydra. It might just have been overly large deep ones. And the protagonist thinking he killed the Big Bad does not mean much, especially in a Cosmic Horror Story with a madman as the narrator.
Castlevania lets you beat the crap out of Death on a regular basis, not to mention some of the more notable Bosses like the personification of chaos in Castlevania: Aria of Sorrow, and all sorts of high-level demons.
A minor, recurring enemy at that. It actually is present in multiple Castlevania games, but is generally named Malachi (mistranslation during production of Castlevania: Symphony of the Night; the name stuck), and never a boss.
At one point in Castlevania: Dawn of Sorrow, you walk in on Dmitri killing Cthulhu/Malachi, so Soma might very well ask the trope title.
And, in both games, you can attack with your bare fists, enabling you to execute a perfectly literal interpretation of this trope.
Castlevania: Symphony of the Night: Shield Rod + Alucard Shield = Did You Just Eat Cthulhu? Especially with Galamoth, a potential ruler of hell who's two screens tall, and you consume him like so much dim-sum.
Galamoth also has an odd quirk where blunt strikes to the face make him flinch. A savvy Alucard can reach an eye-level platform before he's ready to fight and defeat him easily with nothing but repeated punches to the nose.
Chrono Trigger, in which a teenage boy and his friends amass enough power and allies to be able to destroy, in direct combat, a being that renders planets nearly uninhabitable and shatters civilizations. And one of your party members fights with her fists.
And said alien does all on-screen mass destruction its weakest form.
Not to mention, a fully-leveled Ayla can kill its strongest form in two punches if both are critical hits.
As an extra bonus, the Ocean Palace scenario, which is the first time are forced into a confrontation with Lavos, contains several references to the Cthulhu mythos. (You can voluntarily face Lavos anytime after you reach the End of Time, but unless you're in a New Game+ this only leads to a quick Game Over if you do so before the Ocean Palace event.)
Mortal Kombat has Raiden, the God of Thunder. However, he is no stronger than every other fighter, human or not.
The first game explains this somewhat, as it is said that he was only allowed to compete in the tournament after taking a mortal form. Eventually, however, the creators just said "the hell with it" and would go on to introduce more gods to the series like Fujin and Shinnok, who are also no stronger than every other fighter.
He gets punched out at the beginning of Deception, then you punch out the almighty Onaga at the end.
City of Heroes usually avoids this — big threats need big groups of superpowered individuals to take on — but there are a good few moments where really big threats can be taken out with rather questionable means. The comic strips, for example, have two instances of superpowered hordes being taken out by flashbangs on arrows; in the first case a bunch of ancient deathless ghost mages, in the second case a group of psychically enhanced and deranged lunatics about to tear apart a powerful hero. In-game, while not common, it's quite possible for a group of "natural" origin heroes with powers on a normal human's level to take down Lanaru or Ruladak, beings that make up major aspects of a sentient dimension's awareness. That's made worse by requiring that group to spend upward of six hours going through the lore behind those opponents, describing how they literally broke their planet. Even more fun is going home and getting your backside handed to you by a next-gen SWAT team.
Then there is Hequat, Goddess of the Mu, who can be taken on and defeated by a lone villain. (They do at least say that she is in a weakened state, which is why you have to go and attack her now.)
Lampshaded in the third game. According to backstory, humans actually have potential to be even more powerful than angels and demons. That's also a reason why the demons are messing with human world in a first place.
Also there is in-game achievement "Punch Diablo".
In Warriors Orochi, you get to punch out the Serpent King Orochi and, of course he returns. He becomes even more badass in the sequel when you see just how many people he punched out, including an example where Orochi himself punches out a Cthulhu even bigger than himself-The Gods.
An "Did You Just Make Out With Cthulhu" example (see also the Suzumiya Haruhi example) occurs in the good ending of Disgaea 2, when Adell stops the real Overlord Xenon, Rozalin, by Frenching her. Did You Just Make Out With Cthulhu is now its own trope (sort of) - see Divine Date. Sadly, there is no "Broke your dick having sex with Cthulu" trope.
Also in Disgaea 2 you can fight and defeat Laharl (the aforementioned level 1200 overlord). To put it into perspective, Laharl is the protagonist of the first game with enough power to blow up a planet out of hand. And in the PSP remake of the original you can fight Zetta, who is stated to be the most powerful being in existence. Then there's Baal or The Dark Sun...
In the third game, Raspberyl prevents Mao's unleashing of his REALLY evil side (a horror in his own right) by hugging him. TWICE.
Basically, in the Disgaeaverse, there are a number of characters who are fully capable of punching out Cthulhu.
Phantasy Star's chief antagonist is the Eldritch Abomination Dark Force/Dark Falz. In the original tetrology, Dark Force is the manifestation of evil that attempts to invade the Algol system every millennium. Its backstory is different in the gamesthatfollowed, but in any game, it is an enormous monster and intergalactic threat, each time by a team of comparatively teeny tiny heroes.
Doom is one of the legends in this department. The hero, an ordinary Space Marine, with an arsenal of powerful but in no way supernatural weapons, kills his way through hell, defeating archedemons and such.
It ends with Hell exploding and Satan's brain pumped full of rockets. The Marine does not go in for half measures.
In the hilarious Doom comic, the Marine literally tries to punch out Cthulu (in this case, a Cyberdemon), but fails and spends the rest of the comic gathering weapons.
Not limited to the comic book. Doom power gamers prove their skill by performing the same feat in game. Silver medal for using the berserk punch, gold for regular punch.
Quake 1 actually had you telefrag Shub-Nuggerath. You destroy a giant worm-like lava thing named Chthon in the first episode, too.
Dragon Quest games love this trope. Every final boss usually has the whole world scared shitless, generally proven themselves unbelievably evil, and are stupid powerful, and once their asses are kicked, the games in series go out of their way to make sure you know you just punched out Cthulhu, and usually every citizen on the planet is quite aware of just how damn badass you are at the same time.
Hastur from Earnest Evans is, indeed, taken down by a puny human whip.
Averted with the Daedra of The Elder Scrolls seemingly fall into this category. They actually possess no real body, instead creating avatars with which they can then interact with/brutally murder mortals. When destroyed, the physical body remains but their essence returns to Oblivion.
Averted in Battlespire. When confronting Mehrunes Dagon you do not in fact kill him; rather, your weapon allows you to sever his connection to reality, collapsing the bubble dimension and forcing him back into Oblivion
Averted in The Elder Scrolls III: Morrowind. The plan ends up not being about killing Dagoth Ur, which would never work according to others, but severing him from the source of his power - the heart of the dead god Lorkhan; cut off from his power source, his once-again mortal body dies.
In a literal sense, this aversion makes the trope possible, many, many times; a player with high unarmed can literally punch out Dagoth Ur over and over. It keeps him disabled for longer than deadlier weapons.
Hircine actually asks you before the fight to choose which aspect of himself to fight. The implication being that if all of his aspects where to be combined the player would have no chance whatsoever.
Averted nicely in Oblivion when the player finally confronts the Big Bad, Mehrunes Dagon. As you're up against an evil god who just tore reality a new one, the actual fighting is left to your companion, the descendent of a god himself. The best your character can do is stagger Dagon for a few seconds to buy time for Martin to complete his transformation. Unless, of course you hit him with some special attack or your custom-made sword of mob destruction.
Too a lesser extent, the trope still applies, because many bosses such as the King of Worms and Mankar Camoran, and every enemy except Mehrunes Dagon can be easily killed by punching, since Hand to Hand is a legitimate combat skill in Oblivion.
Seemingly played straight in the expansion. In fact, you are merely replacing the avatar of a Daedric Prince; the essence of Sheogorath, his madness and power, are eternal and simply moves to new avatars when he becomes bored.
Played with in Skyrim. Yes, Alduin is the bringer of the end and he was powerful enough that a previous set of heroes could only send him through time. Yes, the player does manage to kill him (quite easily if Dragonrend is used). However, one of his contemporaries (his former Dragon, no less) snarks that he's not really all he claims to be.
It's implied that Alduin is truly undefeatable, and that the Dovahkiin merely strands him in time again, delaying the inevitable; this is mentioned as a reason you didn't absorb his soul.
The Dovahkiin has the advantage of not being an ordinary mortal (he/she has the soul of a Dragon) and being somewhat Immune to Fate since he/she has no set-in-stone destiny. Even Alduin can't fight fate which is implied to be another reason he lost. It's not truly time for the world to end.
In The Elder Scrolls V: Skyrim, you can literally punch out Chthulu, or at least any elder dragon you so desire. Simply use the Marked For Death shout on them. This shout is supposed to lower their armor by 75 points for 60 seconds. Due to a bug, it instead permanently reduces their armor by 75 points per second for 60 seconds. If -4500 armor is not enough to knock out the dragon with a single punch to the face, use it again.
Justified in Eternal Darkness — humanity defeats the Ancients, but they have not one, but twoEldritch Abominations backing them up — one's behind the scenes, and one is summoned to do the actual ass-kicking.
Actually, once you've played the game three times, you find that thanks to the nebulous reality-bending of the situation, you defeat all three simultaneously (despite it being a rock/paper/scissors relationship), and the only one left is dying anyway.
This is the case with most final bosses in the Final Fantasy series:
All the way back in Final Fantasy I, you can literally punch out Chaos (who is at the very least sufficiently eldritch, if not the actual anthropomorphic personification of the concept of chaos) with the Monk/Black Belt class. Chaos is also not invulnerable to White Mage's "FEAR" spell (whose effect is that it causes enemies to run away), though of course the chances of it working without heavy luck manipulation is slim.
After Emperor Mateus of Palamecia (in the world of Final Fantasy II), died, the evil half of his soul went to Hell, where it proceeded to single-handedly slay the Devil and take over his demonic powers. The other half? It went to heaven to become God/Become God. The celestial chain have never suffered a worse punch-out.
Final Fantasy III: The Cloud of Darkness is an actual God which manifests as a roughly female avatar from a swirling, multicolored fog. It has no purpose, no reason, other than to consume all the reality of the World of Light itself. It's beaten back by four kids with a penchant for onions.
Final Fantasy IV: Zeromus is a grotesque, shapeless thing with a vaguely crustacean appearance, and the embodiment of the primal force of Hatred itself. Although Cecil and company defeat it, it claims to be eternal, or, at least, that it will exist as long as humanity does.
Sephiroth, from Final Fantasy VII is said in a Word of God case to be "the strongest character in the Final Fantasy VII universe. There is nothing above him, and it would be impossible to make a character stronger than he is." He's defeated a couple of times by sword combos. Albeit lengthy, very impressive sword combos that attack him from virtually every angle. The eldritch abomination part comes in when you consider Jenova. However, he never really dies, since he came back for Advent Children, and can probably come back again. He can be defeated, but he will come back, that makes him terribly dangerous. Oh, and if you're not sold on the God part, his leitmotif and final form scream the trope One-Winged Angel.
Far stronger than him (in game terms) are the Weapons, in particular the Ruby Weapon, which can instant kill two characters, has incredible defense, and looks kinda like a eldritch abomination with all the tentacles. He can be defeated with a single level 7 character. It's pretty easy, with the right material and heat resistance. Takes half an hour, but what can you do? It is an unstoppable force representing the life force of the earth.
Averted in Kingdom Hearts and its sequel where he is much harder to 'beat', since you don't really kill him. Don't worry, the series has its own Eldritch Abominations to punch out.
A rare example of the player being on the wrong end of this trope occurs in Final Fantasy VIII. If you acquire the allegiance of Odin then he will sometimes show up to instakill whole packs of enemies for you. On the last occasion when the player fights Seifer Odin's summoning animation will play, perhaps leading people to believe that their rival is going to get taken out in a single hit. Seifer proceeds to nonchalantly bisect Odin, forcing players to fight the battle in the normal manner.
Final Fantasy IX: It's not clear exactly what Necron is, since he appears a bit as a Giant Space Flea from Nowhere, but in the English version he claims to be Death itself. (And, of course, he gets obliterated by our heroes because they don't like his "destroy all existence" plan.)
An Honorable mention goes out to Final Fantasy X where in there are TWO Eldritch Abominations. The first and more easily recognizable as actually being an Eldritch Abomination is Anima, an Eidolon who the protagonists have to fight because she (yes that horrifying thing is a she) is simply doing the bidding of her insane son who has mad delusions of marrying the main heroine in order to temporarily save the world from the other more dangerous Eldritch Abomination The other one is the gigantic Space Whale known as Sin who turns out to NOT be the final boss, no that honor goes to a Space Gnat What's worse is that Sin can't be killed because whoever kills him BECOMES him.
The people of Spira worship a mysterious, almighty deity known as Yevon. Yevon is actually evil, and the main villain and final boss of the game (although he technically isn't a god, but rather a ridiculously powerful summoner from 1000 years in the past.)
The avatar-related battles are also arguably an example of this. Although the "prime avatars" are not the real deal, you do actually fight Diabolos, Bahamut, Odin, and Alexander. However, of those, only Alexander is really defeated (even then, it seems you merely halted him). The second Diabolos fight was more of a test to prove your worth, and Bahamut and especially Odin seem more impressed than defeated.
While the final boss is totally a One-Winged Angel, a great deal of the side quests in Final Fantasy XII basically amount to this trope. Particularly Zodiark, who is of the Sealed Evil in a Can variety, and Yiazmat essentially a huge, ancient dragon with 50 million hit points.
Used heavily in Final Fantasy XIV, wherein the player character does this six times throughout the course of the storyline, once to each primal (Ifrit, Titan, Garuda, Leviathan, and Ramuh, in that order) as well as to the megalomaniacal King Mogglemog XII (who might also be considered a primal, arguably). And that's not counting the extracanonical Extreme fights. Your reputation as a god-killer turns you into The Dreaded among the Garleans (During one late-game cutscene, a small cadre of troops run at the sight of you, cowering at the presence of the "Eikon-slayer")
Final Fantasy Tactics has a cabal of six Eldritch Abominations (seven if you include Elidibus) that are either sealed in magical crystals or using said crystals as a gateway into the mortal realm, and each of them is defeated by a group of mere mortals. If you fight them with a Monk in your party or with the Monk's "Brawler" ability equipped, you can literally punch each of them out of existence.
In Crisis Core, you can beat up Minerva. Particularely made a literal example, if the player continuously uses Costly Punch to .. really punch her out.
In Lightning Returns: Final Fantasy XIII, Lightning faces off against Bhunivelze, the sole-remaining God who created a brand new planet and who recruited Lightning to harvest souls to bring into the new world in the final battle, and manages not only to beat him single-handedly (mostly), but knocks him into the Void after he reverts back into crystal stasis.
In NetHack variant Slash EM, it's possible to summon Cthulhu in debug mode. But in Slash Em Extended, the player actually has to beat him for the Amulet of Yendor. He's ungodly strong and revives after a while, but he can be overwhelmed by a decisive offensive action.
Common in the SaGa series, which has a tendency to base bosses on various mythical deities, not just the final ones.
Bosses from the second game are also gods and named from various mythologies (Odin, Venus, Apollo). You beat the crap out of Venus and Odin (who had been resurrecting you for most of the game. On the final world a reanimated statue of Isis joins your party, and you take on a security system built by the ancient gods. However, most of the Gods in the second game are just people with MAGI, aka parts of an ancient statue (yeah, the one in the spoiler above). That you're carrying most of the MAGI most of the game and don't declare yourself a God probably has some meaning to it, but the game just skims over that point.
The bosses of the third game have declared themselves Gods of their world, but they're really stretching the definition at that point. The God of your world would fit the definition if he was trying to be an enemy, considering he used to be one of them. But in the end you only fight him in an attempt to assist his suicide before the final boss takes him over, turning him into some sort of wormy brain thing. Guess how that goes?
As mentioned above, Kingdom Hearts does this a few times. The Greek God of the Dead (or the wisecracking Disney version) is a recurring boss, and while you can't seem to put him down permanently you can inflict some serious hurt. The most powerful Heartless can easily be seen as Eldritch Abominations, as can some of the Nobodies, and, oh yeah, the main characters take on Disney's Chernabog (who is basically Satan) in the very first game. He's not even the final boss, just something the developers kept in for the cool factor. For Sora, Donald and Goofy, fighting the Devil is a speed-bump.
Fire Emblem: Radiant Dawn requires you to kill a god with a mercenary and his posse. Granted, one important member of said posse is a vessel for the equal and opposite half of that god.
You still have to land the killing blow with The Hero's Infinity+1 Sword, or else the aforementioned god will simply regenerate. Justified because Ragnell was one of two swords created by the goddesses back when they were one deity. It is also powered up by said equal and opposite god during Ike's finishing attack.
Even that doesn't kill Ashera. It does destroy her physical form for a several hundred years and during that time Yune is able to recombine with her and they become Ashunera again.
Subverted in Fire Emblem: The Sacred Stones. The previous group of heroes had to seal away the Eldritch Abominationwithin the titular Sacred Stones, which over the course of the game naturally get broken. However, in the closing moments of the game, the heroes seal it away again, leaving them to fight the mindless body but not the full evil. It is implied in the game that they could not defeat it, only seal it, just as the generation of heroes before them had to do.
Fire Emblem: Awakening gets in on this as well, done to Grima who is essentially an evil dragon god. There are even two ways to do it: either you return him to slumber, or you kill him off for good (though the latter requires the sacrifice of your Avatar). Oh, and the reason Grima and his cult are after you is he IS you reincarnated.
At the end of Irrational Games' Freedom Force, the team must contend with Timemaster. Timemaster cannot be defeated until you've destroyed his four Energy Crystally Thingies, but once you have, the Lord of the Timelines is in for a good face-kicking.
Basically the stated goal of God of War is to...punch out the God of War. Sure, Kratos needs to go on a very long quest to retrieve a MacGuffin to give himself temporary godlike powers, but ultimately those "godlike powers" turn out to be "make me really big so I can beat this guy up."
As the original Greek Gods didn't always defeat human heroes (Ares in particular got beat up by Diomedes in one book of the Illiad) this is not entirely unreasonable.
God of War II basically takes this to the extreme: Kratos punches out gods, the gods parents, and everyone that gets between him and the gods. All because he hates Zeus. And because Zeus is totally a jerk.
Also his father, who apparently sired him specifically to take out any other Olympian that rebelled. Zeus is fully capable of this level of Jerkass, especially in this game series.
Possibly more impressive than the above is that he KILLS THE FATES! And this is after they tell him they've seen the future, and in it he fails. This isn't even possible for Olympus.
Word of God has it that God of War 3 explains why the greek pantheon of gods no longer exists. It's no one's surprise that Kratos is the answer. The ending is basically Did You Just Punch Zeus til His Head Was Completely Obliterated?
Most of the big bosses in Kirby games can only be described as an Eldritch Abomination, but of course Kirby thrashes these folks on a regular basis.
Notable examples of this are the Soul forms of final bosses. They're like the final bosses, but much harder, and you can only face them by completing the True Arena.
In The King of Fighters '97, you take down the legendary Orochi, who is treated as the equivalent of a world destroying god in this series.
To be fair, the game also makes it clear that you only put it back to sleep for, hopefully, another couple thousand years. AND it also more or less states that Orochi was using only a minuscule fraction of its power, due to only three of its eight "heads" having been used in its revival, and due to having just woken up. Essentially, had it been at full power, it'd have ripped you apart. Even as weakened as it is, it dishes out a tremendous beating on the heroes.
In the SNES strategy game Der Langrisser, the party, which starts off as only a pair of friends from a small village, eventually grows powerful enough to challenge Lushiris, the Goddess of Light. More accurately, the main character can one-hit kill her if built right. Rohga puts it quite bluntly, in fact: "Holy shit... Incredible! You've even killed a deity!"
Occurs in the endgame of Legacy of Kain: Defiance, where Kain uses the newly acquired power of the Soul Reaver blade to take down the Elder God.
At the end of the prehistoric chapter of Live A LiveThe shaman is eaten by a gigantic dinosaurish thing that the villagers worship as a god. It spits out the shaman's skull and then Gori throws it at him. It's also possible to kill the dino-god with two attacks from the White Mage.
In The Legend of Zelda: Skyward Sword, the final boss is referred to as the Demon King who fought against the gods. Or in other words, the Zeldaverse's equivalent of Satan. He's also heavily implied to be the source of Ganondorf, who is a mere remnant of this being.
Pretty much the whole series can be consider an example when you look the powers of the different characters, and realize that if many of them actually fought the fight would be a big Curbstomp Battle, assuming of course character shields were removed (for example, Captain America going up against the Hulk).
Marvel Ultimate Alliance has the same issue. Your little super team fights nearly every supervillain in the Marvel Universe over the course of the game. As a result, a skilled player can defeat Mephisto, Galactus, Gladiator, Ymir, Loki, and Dr. Doom coupled with the stolen god powers of Odin all with Badass NormalNick Fury.
This does reflect comic book "reality", in which Badass Normal heroes regularly trounce super-powered foes that in a realistic fight would leave them as a stain on the floor.
Somewhat justified in that the fight with Galactus consists entirely of the team running for their lives, and then distracting him while the Silver Surfer turns Big G's own powers against him. And the fight with Mephisto is impossible to win until the X-Man you didn't save forces him into the void with him/her.
Commander Shepard has punched out a few Cthulhui. The final confrontation of Mass Effect 1 pretty much consists of exposing the resident Eldritch Abomination, the Reaper Sovereign, and letting the Human Systems Alliance shoot the bajeesus out of it. However, given that it was only ONE of a race of Eldritch Horrors, and it was being attacked by the combined forces of half the space-faring species in the galaxy, and even then it only barely worked, it's relatively justified.
It's also assumed, in the game, that the thing didn't just reveal itself from the beginning precisely because it was afraid that something like this would happen.
Not assumed, it's said outright. By the Prothean VI very near the end of the game.
Mass Effect 2 on the other hand, ends with your three-man team fighting a Reaper, albeit an unfinished one, on foot. It was 'EPIC!
Its actually possible to beat the nigh-unstoppable Brutes to death without fighting a single shot. In fact, Vanguards even get a special award if when a Brute tries to charge at them... they biotically charge right back.
The final boss of the Xbox remake of Ninja Gaiden wields the Dark Dragon Blade, which is supposed to give him the power of the "Devil incarnate". While he is a rather tough fight, our Charles Atlas SuperpoweredHighly VisibleNinjaBadass protagonist still defeats him anyway. Admittedly, Ryu was using the True Dragon Sword, which was meant specifically to counter the DDB, but still. Ryu also takes down multiple Greater Fiends, each of which is worth quite a number of regular fiends in power, as well as the released Archfiend.
This is the entire point of the old Bungie game Pathways into Darkness — you play as a special forces operative sent to nuke a gradually awakening Sleeping God unconscious before it can awake fully and unleash unimaginable havoc.
The last game in Bungie's Marathon trilogy averts this by having the protagonist travel through dimensions and/or back through time to prevent the Eldritch Abomination from ever being released in the first place.
Subverted in Peasant's Quest: "beating" the game consists of the protagonist getting closer than any hero ever has to killing Trogdor - deflecting one gout of flame, stabbing your sword an inch or two into Trogdor's nigh-impenetrable hide, hearing The Burninator speak, and finally being almost effortlessly burninated. A really cool monument is built to honor this feat.
In episode 5 of Strong Bad's Cool Game for Attractive People, Strong Bad actually does defeat Trogdor by hitting his weak spots, which Rather Dashing failed to notice. Sure, Strong Bad transforms into a big, muscular version of himself with a gigantic knife (displayed in ridiculously awesome next-gen graphics) to accomplish this, but he's still just hitting him... And then it turns out that it was all a dream and Trogdor is still destroying the countryside.
Played for laughs in the first episode of Penny Arcade AdventuresOn the Rain-Slick Precipice of Darkness. Inciting Gabe to tackle a very Cthulian being, Tycho asks "Do you want to punch a god?" Gabe: "..." Tycho "..." Gabe: "..." Tycho: "..." Gabe: "Yes!"
Then again in the second episode. PC: "Gods? Again?" Gabe: "Yeah, it's like... I don't mind fighting gods? It's just I'd like a little warning first."
Just to put things in perspective here? The first God is defeated through a combination of a radio tube, absolutely pure urine, and the soul of a mime. The second is defeated with a giant robot doll piloted by a thirteen-year old girl.
In Perfect Dark Zero, Joanna Dark defeats Zhang Li with early-21st-century weapons though the knife/machete comes in handiest despite the fact that he uses the Graal to gain superhuman powers and "become a god".
In the Pokémon games, you are able to capture legendary one-of-a-kind (per game) Mons that are often forces of nature. Pokemon Diamond And Pearl of games contains Arceus, who apparently created the universe. In order to capture Pokémon, you have to attack them, lower their health, and give them status effects before you can do so, which is what makes it this trope.
The 2D fighting game Pray For Death had Cthulhu himself as a normally playable character.
Your final opponent in Puzzle Quest is Lord Bane, the god of Death (who responds to his defeat by basically saying he'll just regenerate in a century or so and wipe out your descendants... just like he did last time.)
In the first Shadow Hearts game there are two different villains who try to summon a God, the first to destroy the Japanese army and the second to cleanse the Earth of sin by destroying the wicked. By the start of the second game the new villains refer to the hero Yuri as "Godslayer".
Not only Yuri, but Koudelka (in the manga) also manages to control a monster by hypnotizing herself, before she possessed by that monster. She then used the monster's power to beat up the Smug Snake that tried to destroy the world using that monster's power.
The videogame Shining Force subverts this in the final fight with the Dark Dragon. Even after depleting its hit points, it's still not technically dead, and the best that can be done is for the main character to stab his sword into the back of its head, and hold it there while the rest of the party escaped the collapsing castle.
The final boss of Shining Force 2 is a demon who is effectively the equivalent of Satan. More humorously, there's an exploit involving the master's monks where you cast their buff skill, earning 48 exp, than leave the battlefield. You can keep doing this till the monks are lv99, at which point, they will be stronger than said demon, leading to a literal Did You Just Punch Out Satan.
At the end of Silent Hill 3, Heather takes down God. With a lead pipe.
It should be noted, however, that the games are hardly clear on what exactly is the "God" of the town's religion, and indeed it's entirely likely to be yet another hallucination (which is one of the more reasonable Epileptic Trees concerning the game).
The local Eldritch Abomination gets punched pretty much once per game, but what the result is depends on which of the endings you get.
In the UFO ending, aliens laser-carpet-bomb Silent Hill itself (i.e., the entire town) from orbit.
It should be noted that the God was born incomplete, and from the wrong body. Claudia wasn't capable of birthing the God at its full potential, as Alessa was; or how Heather is now. Had the God been born as it should have, whether it's a delusion or an actual demon, it's doubtful Heather would have been able to beat it. That's what happened in the first game as well, with the God being forcibly ripped from its incubating vessel by aglaophotis. Also, even though the fans love to use the steel pipe, realistically the uses of that weapon would be limited once you got to some of the tougher/bigger monsters like the Scrapers, which are armed and deadly close-up. A weapon like that against a big creature that shoots fire and hits hard at close range doesn't sound like a really good idea. Heather would be better off using a handgun or shotgun, which would work to kill a prematurely born god in keeping with the first game ( assuming we ignore Harry's diary of the creature "falling dead" without one move). He did get punched out, but there was a reason in the story and it probably wasn't with a simple lead pipe.
Silent Hill 4: Walter is considered to be a god within the rules of the world he's created for himself. His spirit form completely controls the world and is able to warp things to his liking with his powers. Yet Henry manages to hold him back with simple weapons and somehow plant the eight spears necessary to 'humanize' him without Walter getting in any good resistance, and he's limited to just guns and a chainsaw. (You don't even have to attack him; just go right for the spears and Walter goes down as easy as a Borg shot with a modulating phaser). Even without his immortality though, Walter should still have enough power to easily slap Henry away and end his threat, with him still being tougher than an ordinary human. Yet Henry still manages to kill him rather lamely, even in the Really Bad ending where it's only temporary and Walter comes back to kill everyone in the building. Either Walter doesn't know how to fight, or else the developers didn't know how to have a very average protagonist (Henry) engage such a powerful being and win without giving him some huge advantages and keeping Walter's powers at a minimum.
Walter wasn't the god of his world, but it was the Room itself. Walter just wanted to be with his "mother" (the Room itself) and his whole quest was for giving the Room itself a conscience. Reason why Walter, even though he's the creator of the nightmare itself, is not that powerful: he never focused of making himself "stronger", but instead on giving the Room itself a conscience. As an added moment of Bad Assery on Henry's sakes, he was never really took into account in the whole process and even so managed to stop it by sheer will: no cult text ever took that into account, reason why characters like Henry and Harry were able to destroy the self-conscious inner worlds with relative ease. Jason, on the other hand...
The first non-Robotnik final boss Sonic fought was the watery god of destruction, Chaos, in the first Sonic Adventure. Granted, he didn't actually destroy Chaos, but he did use himself as a projectile and shot through his brain a couple of times.
Kinda justified, since at that point Sonic and Chaos were using the exact same power source, just a different attitude to activate them.
In Sonic and the Secret Rings this trope is also shown (quite literally), where The genie and evil villain the Erazor Djinn uses all the rings to turn into a Horrific monstrosity called "Alf Layla wa-Layla" (Basically, one thousand and one nights in Arabian.), and begins to recreate the world in his own image, only to be stopped by Darkspine Sonic. Meaning, you knock his own attack back at him, fly up, and start punching the holy hell out of him.
In the Wii/PS2 version, you have to make him punch out Dark Gaia manually. Emphasis on the words "Punch-Out!!".
The Soulblazer trilogy has a trilogy of this trope - In Soulblazer, you kill the powerful demon/god(?) Deathtoll with the Soul Blade (admittedly the most powerful sword in the whole world. In Terranigma, you defeat the evil god Dark Gaia with what is essentially a SPEAR, and most heinously of all in Illusion of Gaia you also defeat the evil god Dark Gaia with nothing but your own ectoplasmic arm (as Shadow)!
Even if you use the gothic lolita in Soul Calibur IV, you can defeat a Physical God who not only tamed Soul Edge, but actually created its counterpart.
Splatterhouse sees Rick doing battle with living embodiments of evil and all that serve them... with his fists. And on occasion baseball bats and two-by-fours. Thing is, this is presented in a much more serious manner than usual - the only way Rick can do all this is that the Terror Mask is backing him up, and the Mask is using him as a tool.
Dark Brain from Super Robot Wars and the related series Great Battle IV can travel multiple dimensions using his own powers, grows larger based on the despair of the people fighting it (which, in retrospect, may not be a good thing when fighting mecha pilots), and can destroy planets easily. He seeks the 12 keys of the Super Robot Wars Multiverse, and he created Dynamis the Big Bad of Super Robot Wars R to search and destroy Fighter Roar. You have an assload of giant robots. Guess who's not walking away from this fight?
Same with Irui Ganeden, the spirit of the earth, in Alpha 2, and Keiser Ephes in Alpha 3.
Well, one might say a lot of Super Robot Taisen games feed off this trope. Other games have the Super Robot team go up against villains who, in their respective series, proved to be impossible to defeat... and win all the same:
In the Alpha series and in MX, during the Neon Genesis Evangelion storyline events, the heroes manage to defeat the Seele's Mass Produced Evangelions. Yes, exactly the monsters who, after having been defeated by Asuka, simply regenerated and tore her to pieces as if nothing happened. The Super Robots managed to kill them all. Not only that, but, in Alpha 3, they follow it up by fighting -and defeating- the fusion of the nine white Evangelions with a berserk Unit 01 and the Tree of Life... also known as God! And it's not even the final stage!
Super Robot Wars Alpha also gives a few villains from other series their own moments against the Angels. When the Third Angel appears over Tokyo-3, out steps a man in a suit smoking a cigar. This man proceeds to pound the Angel flat with his bare hands. The man in question? Alberto the Shockwave.
In Alpha 2 and J, during the final assault on Orphan, the Super Robots defeat Baron Maximillian'sHyper Baronz from Brain Powerd. In the series proper, the Hyper Baronz was so powerful that all Hime managed to do was damage it somewhat, and she and Yuu had to wait it out and survive until Baron exhausted all of her energy.
In Tales of Legendia, the heroes beat Schwartz, supposedly a destroyer of universes. To be fair, she needed the negative energies of people to power up, and was weakened by positive energy, ala Earthbound. So her status might have been * very* exaggerated. Or she was just an avatar of the real one.
She wasn't actually stated to have that much power on her own. She was go to destroy the universe by destroying this one point, which if destroyed, destroys everything else.
Again in Tales of Symphonia, the heroes defeated Mithos Yggdrasiil. This person SPLIT A WORLD IN HALF, and in the first battle you fight against him, he punches you out with a healthy serving of Beam Spam. The second, third and fourth times you fight him, however, it is essentially a Curb-Stomp Battle in your favor, making the Big Bad look like a Squishy Wizard.
Tales of Eternia goes one further and gives you a final battle against Satan. Well, his fantasy counterpart, but it's still impressive.
Jude Mathis literally punches the REAL Maxwell, Lord of Spirits, right off his throne in TalesOfXillia.
Tales of Destiny 2 one-ups all these. The entire endgame is about the heroes deciding whether or not they should kill the goddess of time to reset the timeline. They do, after a long grinding boss fight. In short, gods tend to not have very good life security in the Tales Series.
In Touhou, Plot Armor has allowed Reimu and/or Marisa to defeat and subsequently befriend beings that while not eldritch or abominations are certainly comparable to them, including but not limited to an Enfante Terrible with the power to destroy anything just by thinking about it and clenching her fist, one of the four Oni Devas that hurls black holes and is capable of tearing apart mountains, the millenia-old ruler of the netherworld, a Reality Warper with likely limitless power, one of the Judges of the Dead, and a nuclear-powered hell raven that uses miniature suns as a weapon.
They also defeated five literal gods in Touhou 10 (though two were just harvest gods). The next game's final boss (who already made the above list) had eaten a god to gain its power. Then again, in Touhou-verse "god" doesn't really mean all that much.
Of note is one of the sub-plots, in which cute little ice fairy Cirno was only looking for a ghost-free place to happily frolic around and have some fun... defeating in the process an insanity-inducing rabbit, the two aforementioned superpowerful girls, a faster-than-wind raven girl, the ferryman of the Netherworld's river, and the Judge of the Dead herself.
Tohno Shiki from Tsukihime has a power that is very conducive to this. He arguably does this by making Roa Deader Than Dead, which is one hell of an achievement considering the man regenerates from just his ankles at one point; to add insult to injury, Shiki destroyed Roa's concept of existence, which prevents him from reincarnating as usual.
In the backstory of Tsukihime, the mage Zelretch is famous for being a True Sorceror, known for travelling between realities at a whim... and for killing Brunestud of the Crimson Moon, also known as Type-Moon, the Moon's Ultimate Being, the greatest life form created by the Moon with the total power of that celestial body behind him. The details aren't explained, but apparently it involved dropping the Moon on Brunestud's head. He might have gotten turned into a vampire for his trouble, but he still defeated one of the most powerful beings in the universe, by himself, using only raw power. For contrast, Type Mercury, known as ORT, is a giant crystal spider, powerful enough to override reality with its own internal Mental World and obliterate vampire kings in an instant. It is also explicitly the most powerful being in the present Nasu Verse timeline. Types are also alien enough that even Shiki, that Cthulhu-puncher extraordinaire, would be unable to kill them, because their concepts of death are so unrelatable to Gaia; the only way to kill ORT is by pure force, which nobody in the Nasu Verse can currently bring forward.
Actually, to clarify this a bit, Type Mercury/Ort technically has the "highest raw attack power". Take that how you will.
And technically, judging by Notes, the Black Barrel could theoretically take out ORT. Or make it so that Shiki can see their lines of death, since the Black Barrel apparently "forcibly injects a concept of death" into the target, making it basically super effective against all the Types and pretty much everybody else come Notes. It's called the "God killer gun" for a reason.
In Notes the Black Barrel could indeed do that but it's pretty much useless with the death of the last human on the planet.
In Valkyria Chronicles, with Squad 7's defeat of Maximillian. He had equipment that mimicked the powers of the Valkyria and unlike the fight with Selvaria, Squad 7 decided not to rely on Alicia's Valkyria powers.
World of Warcraft raids let players duke it out with all kinds of eldritch horrors and the mightiest beings in the game lore (only short of Sargeras), only with larger numbers than usual. Some of them are said to be in a weakened state or to be merely banished when defeated but many of them put up a hell of a fight.
Many of the Old Gods of Azeroth have been turned into raid encounters. The first and most notable was C'thun who, even with the massive power increase for players since his release, remains a dangerous opponent. He is still killed on a fairly regular basis, however.
Another Old God, Yogg-Saron, was added in a patch. In this case only the hardiest can defeat him without help from super-powered guardians left by the Titans.
One of the raids in the Caverns of Time has you go back and fight Archimonde the Defiler. The demonlord in Warcraft III: Reign of Chaos that could not be stopped by ENTIRE ARMIES at the end of the Night Elf campaign. However, the encounter ends the same way as in the original game once the players weakened him enough. He's also one of those bosses that can easily kill an entire raid in seconds if you don't know what to do.
It's not just the player characters, either; the Drakkari trolls in Zul'Drak have been practically eating their own gods to gain the power to fight the Scourge. The degree of success they have is varied; one god just dies and they take his power, another is saved by the player, a third one takes her traitorous servants with her to a personal hell. One god is actually seen being taken down in a single magical "hit".
In The Witcher Dagon getting killed by Geralt at the end of chapter 4 is pretty inevitable, as you can get him in the bestiary by chapter 2. Interestingly, the god isn't defeated directly, but by killing his worshipers, depriving him of prayer.
Not to mention you're also able to fight the King of the Wild Hunt, a supposedly immortal personification of death itself, after beating the Big Bad if you completed a certain quest during the fourth act.
In the books the Wild Hunt pestered Zireael and had run-ins with unicorns.
In the World of Mana, high-tier supernatural beings are common boss battles:
X-COM: Terror from the Deep has a partially justified version of this. The "Ultimate Alien" cannot be defeated once he wakes up, but you can kill him by blowing up the power generators to his cryogenics system first. The explosive result, however, makes theearth uninhabitable.
The biggest threat to humans and Vasudans in Freespace is a powerful Shivan dreadnought, the Lucifer, with nigh-impenetrable shields, which devastates Vasuda Prime and is looking for Earth. It is only defeated in the last level through the use of Lost Technology by chasing it in subspace with fighters/bombers and destroying its generators while its shields are down. The explosion does, however, cause Earth to be but off from the rest of the galaxy for many decades.
The sequel had the Shivans go Up to Eleven in terms of threat level: your biggest victory in the campaign comes when you destroy the Sathanas, a ship far more powerful than the Lucy ever was, at great cost (the one ship capable of tackling the Sathanas is drydocked for extensive repairs). Then the Shivans reveal that they have over 80 more such ships en route to Capella.The Alliancedoes not walk away with a victory.
According to the running backstory, Master Hand and Crazy Hand represent the twin gods of creation and destruction, yet it is still possible for players to beat them. In classic mode, it can be seen as a friendly sparing match, but in Brawl's story mode, Master Hand is visibly subdued and enslaved by Tabuu, who can be seen as a devil entity, and whom the player can also beat. In Wii U/3DS, Master Hand can turn into Master Core, a Shapeshifting straight-up Eldritch Abomination which, again, can be beaten by any fighter.
Wii U/3DS adds two Physical Goddesses as playable characters: Rosalina, Mother of the Cosmos, and Palutena, the Goddess of Light. Due to their playable status, they can naturally be beaten by anyone else.
Heinrich I in Return to Castle Wolfenstein is an ancient Sealed Evil in a Can. Supposedly indestructible, the only way to defeat him was for a wizard to seal him in the ground. Of course, that was way back around the year 1000, so when the hero shows up in 1944 it quickly becomes evident that being invulnerable to swords and spears is not the same as being invulnerable to nazi superweapons
Wolfenstein Spear of Destiny has you shoot down the angel of death, requiring a non-stop chaingun firing at pointblank range for a WHOLE 10 seconds.
The third campaign of Guild Wars, Nightfall deals on how the human heroes manage to overthrow the fallen god Abaddon, even when in the penultimate mission the other gods themselves decline to directly intervene, arguing that the humans have all the strength they need.
Given the fact that humanity's ability to fuck up the plans and creations of gods is why the gods basically went into retirement, this kind of makes sense. "Well, they shat all over everything we did before, just give one of them our blessing and they'll probably find a way to fuck things up for the Big Bad as well"
And Guild Wars 2 will involve defeating at least one of the ancient dragons (Eldritch Abominations at least as powerful as the gods). In fact, getting back to the other two continents (as we'll inevitably do in expansions) will require it: Zhaitan (set up as the Big Bad by the trailer) has pretty much blocked off sea travel by way of his zombie pirate Mooks, and another dragon (Kralkatorrik) is blocking the land route to Elona.
It's quite possible that Grenth did this when he overthrew Dhuum, as well.
They're both gods, so that's more of a "Did Hades Just Punch Out Thanatos?"
The Lord of the Rings: The Third Age, which is set during the events of the movies but tells a distinct story, hasthe party instantly transported to the top of Barad-dűr, where they fight spotlight-eye Sauron (who is a lesser god), and beat him into submission using swords, spears, and arrows. This is preceded by the party killing over a dozen ringwraiths as well.
In Thief: The Dark Project, Garrett kills the Trickster, a forest god who resembles Pan. With a magical bomb. At least it was an inventive way to defeat the end boss, which fit well with the style of gameplay.
Garrett even lampshades it in the stage intro to "The Maw of Chaos", saying "I've never robbed a god before. It'll be a challenge".
Thief: Deadly Shadows has a hidden Eldritch Abomination as the Big Bad, who emerges from hiding as you enter the endgame. This being CANNOT be harmed by ANYTHING...until you literally erase her magical glyphs.
In Dead Space, the final boss is the Hive Mind that is controlling the Necromorphs; it has to be at least over 100 meters tall. Isaac Clarke is an engineer with a headful o' crazy and a cutting tool. Guess who gets owned?
Isaac outdoes himself in Dead Space 3, in which he takes on a freaking moon-sized Necromorph. Okay, technically "the Machine" did most of the actual work there, but this sequence still involves gouging out the Brother Moon's eyes with telekinetically-thrown Markers.
And of punching him out doesn't float your boat, how about riding on his back and using him to kill a Leviathan?
The addition of adjectives in the sequel serves to increase the number of ways with which Cthulhu can be dealt. For example, this video, in which the appropriate response is, "Did you just milk Cthulhu?"
In Ghostbusters: The Video Game, the boys take out several entities that their scans classify as "Deity [Supreme Being]", including the Imprisoned Juvenile Slor, several ascended humans such as Azetlor and Shandor the Architect and, of course, the returning Destructor Form of Gozer the Gozerian himself, aka the Stay Puft Marshmallow Man (although they claim that Stay Puft is weaker than he was when they fought him before, in the movie).
If you win the final battle, you hear Egon lampshade the trope by saying, "We eat gods for breakfast!" Afterwards, Egon things it was too bombastic, but Ray thinks it's actually quite cool.
The final boss of Neverwinter Nights: Hordes Of The Underdarkis Mephistopheles, the second strongest devil in the universe.
If anything, the sequel's Epic level expansion Mask of the Betrayer gets one even better, especially if you were already familiar with the Forgotten Realms campaign setting. DID I JUST EAT MYRKUL?!?
NWN2's first campaign ends with killing an ancient Pure Magic Being. The second expansion Storm of Zehir ends with killing an avatar of the yuan-ti god of poison.
The fight against the mighty Nihilanth at the end of Half-Life. A giant bio-mechanical psychic being of unimaginable power that controls an entire dimension's worth of aliens... taken out by a scientist wearing a fancy suit.
Not to mention that despite all the fancy guns at Freemans disposal, the final blow is best delivered with a good ol fashioned crowbar.
Also carries over to Opposing Force, in which a living biological resource factory that literally sucks matter from our world to make more Race X... is destroyed by one Marine with a sniper rifle.
Both of those are nothing compared to the beginning of Half-Life 2: Episode One, when the previously unstoppable G-Man, capable of casually manipulating time and space to his whims, is completely owned by a group of Vortigaunts (the face he makes is priceless, by the way).
The Vortigaunts are currently keeping the G-Man at bay, and are at least powerful enough to face him on equal terms. However, the G-Man is figuring out how to get past their defenses. The point still stands: up until now, the G-Man was unstoppable in his efforts to manipulate Freeman and the world for whatever it is he's planning. For the first time, he's on the defensive and is now forced to improvise.
EverQuest has a long-standing tradition of making the game universe's gods into major or final bosses. Of course, since they generally don't stay dead in the game's storyline, some have come back for more (and more, and more) as the game has had expansion packs added to it.
Mario & Luigi: Bowser's Inside Story has Bowser go up against a being of pure darkness using his form that has more than enough power to destroy the world, and repeatedly overpowers it with brute strength alone. The only part the Bros. play in the battle is helping to make sure it doesn't get back up again after Bowser has knocked the core out of its gut (he wins at inhaling the thing, too). Did you just prove yourself better than Cthulhu at everything he tries?
And then, in Mario & Luigi: Dream Team, The final boss is Bowser as a Reality Warper, possibly more badass than ever. Then the Mario Bros come along and fight him. For the first time, there's no Eleventh Hour Superpower for Mario when the final boss shows up. The Mario Bros fight him head on, with the only help they get being a bit of healing at the start of battle. Being Mario and Luigi, they win, but it's still one of the most powerful foes they've ever faced.
"CRUD! You dumb video-game heroes ALWAYS pull this stuff! It's RIDICULOUS!"
Mario can kill the goddamn sun in Super Mario Bros. 3. It's fair to say this overshadows anything else that's happened in this series in terms of sheer ludicrousness - and probably many entries in this article, to boot. It helps that the sun is 1) not 93 million miles away, but anywhere between a few yards above the ground to almost on it, 2) not millions of times as large as the planet, but barely bigger than Mario himself, and 3) dead in one Koopa shell. There are Mooks tougher than that. Killing it doesn't have any effects on the world, and it's not even a Boss, just an enemy that appears in two levels only. You could say the real question is: Is Cthulhu Really That Wimpy?
But it's later played straight with Planet Eater Guhnash. It's justified by the fact that you're attacking his weak point, his brains, For Massive Damage, but it's still just one kid and a couple of dinosaurs taking out a being the size of a planet by scratching at it.
In Penny Arcade Adventures Episode 1, after Tycho learns what the mimes are up to, persuades Gabriel and the Player to help stop them from incarnating an Eldritch Horror. To convince Gabriel, Tycho asks him, "Would you like to punch a god?" Gabriel is immediately up for it.
They do manage to beat Eldritch Horrors in both released episodes. With naught but their fists, garden tools, and a Tommy gun.
The Lufia series revolves around the hero Maxim and his descendants repeatedly killing the four Sinistrals every time they reincarnate.
Bayonetta hits her world's Cthulhu out so hard that she punches its soul out of its body. She punches God's soul out of its physical body and into the sun. More accurately, she summons the setting's version of Satan to do it.
Cryostasis does this at the end: Over the course of the game, the main character has altered history so many times that by the end of the game, the Timey-Wimey Ball has finally had it and decides to do away with the player character. How, you may ask? By throwing Chronos, the goddamn God of Time at him.
Inverted slightly in Heavenly Sword: in the end, Nariko temporarily becomes a god. To defeat her, Bohan becomes a deity himself. Of course, since he's the villain, it doesn't work out as neatly as he'd hoped.
The major Big Bads in Titan Quest are Typhon, supposedly the mightiest titan to fight against the gods, and Hades, god of the dead. Zeus Lampshades this after the player defeats Typhon, noting that if mortal heroes are capable of such feats, the gods can no longer be of any relevance in the world.
Princess Maker 2: Lizzie Shinkicker killing the God of War in the LP anyone? In the actual game its more just knocking him out long enough to nick his sword and run past him.
In one of the branching paths in Guardian Heroes, God appears as the final boss...and yes, can be killed.
Dantes Inferno begins with Dante punching out The Grim Reaper. He then slaughters his way through Hell, killing several major demons and eventually beats down Lucifer himself.
Pretty much every fighting game based on a popular anime falls under this where the Big Bad or The Hero can be defeated by a character they would Curbstomp in the actual series. The most extreme cases are in the Dragon Ball Z fighting games that have Mr. Satan in him.
In the Final Battle of Dragon Age: Origins you slay the Archdemon, an ancient dragon god of the Tevinter Imperium in this case Urthemiel the god of Beauty corrupted by the darkspawn taint. Of course, finishing it off requires either a Heroic Sacrifice from a Grey Warden. Though in this case Morrigan provides a way out...one that gives her a chance to raise the dragon god as her own child.
Tekken 2. Final boss fight. Did you just punch out the Devil?
The battles against Ogre (3, TTT2), Unknown (Tekken Tag Tournament, TTT2), Jinpachi (5), and Azazel (6) can also qualify.
In Rune Factory 2, the final boss, who causes earthquakes and can destroy the world is beaten by an 8 year old kid. If you level your character up fully, and use the best equipment, this Big Bad will fall without much effort.
In Dungeon Crawl you can go through the gateway to Hell, and individually beat all four lords of hell. Theoretically you could do this with your bare hands, though they have ludicrous hit points and AC, and, in the meantime, you would probably be killed by the hordes of demons they summon.
What about killing Jiyva???
Gene in God Hand does this quite literally. You defeat Angra (who's basically Satan in the game's universe) by punching him. A lot. Hell, even before getting the requisite Eleventh Hour Superpower, Gene had to beat down three ancient demons with his bare hands to reach the Final Boss in the first place!
Several of the final bosses in SaGa Frontier can probably qualify as gods or Eldritch Abominations. If punching's not your cup of tea, grappling moves work just as well on a region destroying giant mech, Satan, and what is more or less the god of sex.
Almost every boss on Grand Chase's Xenia is a god of some kind. And only one of them said they were going easy on the group.
Likewise, most of the bosses you fight in Aquaria are also gods of some sort.
In Wild ARMs 2, your party has to kill a parallel universe that's encroaching on their reality. Logic dictates that you cannot punch out a universe, but the heroes find a way that almost manages to make sense. Then, after kicking its ass, the main character takes a moment to duel a completely unrelated and comparatively mundane Eldritch Abomination.
Arc The Lad is a rare case: while the Eldritch Abomination responsible for most of the trouble is eventually defeated, it takes four games, 4.000 years in story, no less than five team of semi-godly fighters powered by the local gods and three near or complete collapse of civilization before the Big Bad finally bite the dust. Before that, the game series will provide plenty of deaths, tragedies and Difficulty Spikes: The Eldritch Abomination will eventually get defeated, but you're going to earn that triomph
Every Contra in general. Up to two shirtless men or clad dressed women are to take out a whole army of aliens which includes loads and loads of monsters that are at least 3 time bigger than them with inter-changeable rifles.
Agarest Senki may trump the other examples in here because in this game, you punch out six of them. Although, only two deserved to be punched in the face, and the rest just got dragged along.
Agarest Senki 2 however plays with this one. While you see that Weiss kills Chaos in the opening, punching him out is a bad idea in this game since it caused a lot of problems to the other people. This get subverted when it turns out Weiss did not stab Chaos. He was still discussing stuff with Chaos when fellow Cthulhu Mobius (disguised as Fasti the archaeologist) stabs through Weiss to stab Chaos. If you go to the True End route, this trope then gets played straight again by punching out the 6 gods including Chaos and Mobius. Your head hurt yet?
Myth: The Fallen Lords is about a world where the forces of good and evil each own the world for a thousand years, and then it flips. Unfortunately for the player in the first game, it's the other side's turn to win. The game ends bleakly as the last remains of the good army sacrifices themselves to beat the prophecy and Screw Destiny. This involves killing the equivalent of three gods, and an actual god. The sequel is about the surviving forces of light coming up against the surviving forces of darkness, while destiny and fate have gone Off the Rails, and it also involves fighting godlike creatures.
In the FPS/RPG Strife, your struggle against the Evil EmpireCult called the Order eventually ends with you killing their god, the Entity.
Spyro and Cynder manage to kill the Destroyer, a mythological monster whose meant to destroy the world when it awakens, by destroying every dark crystal in its entire body, including flying into its body and destroying its heart. Malefor restores it to life himself, but doesn't count as Broke Your Arm Punching Out Cthulhu since the 'Cthulhu' in question would've been dead for real had Malefor not been there to revive it.
According to Devil May Cry lore, The Legendary Dark Knight Sparda did this on at least two occasions—demon kings Mundus and Argosax the Chaos. In the first and second games, Dante follows in his dad's footsteps. While Dante needed some help from his dad (or more specifically, his father's sword) and Trish to defeat (and seal away) Mundus, the latter fight was a Curbstomp Battlefrom start to finish. He also takes down the Big Bad of 3 (who was drawing on Sparda's power) alongside his twin brother Vergil, and defeated a demon of similar caliber in the anime.
Grolla also punches out Iris in Rosenkreuzstilette Grollschwert despite her absolute power, unparalelled brains, and claims to be a child of God himself. And, all she needed was the Demon Sword Grollschwert, which basically told her to spill her blood. And she didn't even care if Iris was a god, a human, or even an insect - she was willing to rip her apart just the same. Whoa.
It gets better in Freudenstachel. After Iris hijacks Tia and forces her to fight her friend Freudia, the latter gets extremely pissed and decides to take Iris's defeat Up to Eleven by freezing her in an ice crystal with the intent to put her down for good.
The final battle of Serious Sam: The First Encounter. Sam Stone, an average human, has just fought his way through THOUSANDS of supernatural or alien monsters only to find something horrible teleport in behind him: Ugh-Zan III, a 350 foot-tall, lightning-shooting, Made of Iron, fireball-throwing alien warlock of near godlike power. It's actually somewhat justified, since for the first part of the fight you just run away, the second part you injure him heavily with some semi automatic rocket launchers and uranium cannonballs, but still not kill him, whereas the final part has you trying to hit with a beam from the sky that's implied to be supernatural in origin (since it's coming from a Sirian spaceship and the Sirians use "technomagical" weaponry). If you don't do that, he'll just regenerate his health, making him effectively invincible. To add insult to injury, NETRICSA describes Ugh-Zan III as an ancient deity and one of the most powerful beings in the universe.
Disciples II, particularly the final level of the Mountain Clans campaign, in which your Viking-expy dwarf hero parties must defeat "the wyrm Nhidogg," a physical manifestation of the corruption and imminent destruction of the world due in large part to the dwarves' negligence of their traditions, with weapons. Given the emphasis on martial bravery in those traditions, it makes at least some sense.
Also, the capital city of each side is protected by a "guardian" character who cannot be removed from the capitol, is clearly intended to be effectively unkillable, and attacks in a non-blockable fashion for the maximum possible base damage per hit, but can be defeated with the right cheesy tactics.
In Kingdom of Loathing, one of the monsters lurking in Fernswarthy's Basement is an nth dimensional horror. It starts a being four dimensional and goes from there. And while it gets stronger as you go down, the 4th Dimensional Horror can be beaten by someone who is having trouble with the Bonerdagon.
There are also some very tough bosses in The Sea: Shub-Jiggawat, Elder God of Violence, Yog-urt, Elder Goddess of Hatred, and Dad Sea-Monkee, who's been given terrifying eldritch powers by being hooked up to some kind of machine.
Can happen to Pretenders in Dominions, if they die particularly ignominiously. Some have even been lost to blood slaves... which are roughly the weakest unit in the game and really only exist to give Blood Mages something to sacrifice in combat.
The final battle of Asura's Wrath involves a hand-to-hand battle with the Vlitra Core, the malevolent Genius Loci controlling the Gohma, residing in the center of the planet. This being Asuras Wrath, you do literally punch it to death.
The true final battle, however, comes at the end of the DLC chapters, where Asura quite literally punches out Chakravartin, aka GOD.
By the end of Dark Souls you'll have torn your way through every previously establish bad ass, including several demigods, at least one dragon, huge demons, and multiple outright gods. The in-game justification is that none of them are at full strength anymore. The player character is also the inheritor of a unique Lord Soul, the Dark Soul, making him/her just as much a god as any of the others. Possibly more so, since his/her Lord Soul is at full strength.
One of the possible final bosses of Poacher is the leader of a civilization of what are essentially embodiments of pure evil. The other is the god on which all religious deities that judge the dead (e.g. Anubis, Minos) were based, and - though how directly is up for debate - the source of that civilization's magic and life force. Both of them can be killed with nothing but a 12-gauge shotgun, and only one of them is as tough as it sounds.
The true final boss in Duel Savior Destiny is God himself and is absolutely unkillable by any means as well as essentially omnipotent. However with a little powerup or ten thousand Taiga is able to apparently curb stomp his opponent if the after battle commentary is anything to go by. He still has to do it over and over again due to the whole unkillable thing, though.
The Tekken 2 canon ending has Jun Kazama quite literally doing this to Devil.
Albion: The leader of the Kenget Kamulos turns into an avatar of Kamulos, the God of War, to fight the player characters. And, well, it's not a Hopeless Bossfight. Especially humiliating when the Kenget are always going on about their martial superiority, and their then god is beaten by a party including females, non-humans, and warriors using physical weapons (ie. non-spellcasters), all of which they disdain, plus one traitor of their own people.
In Champions Online, it is quite possible to punch Kigatilik, god of ice and snow, with either powers from the Brick or the Martial arts power sets.
Messiah sees Bob, a tiny cherub angel, managing to kill Satan, or at least thoroughly kick his ass. Granted, it's because of a very contrived plot device where Bob's possession powers happen to somehow create projectiles that can kill this enemy.
Xenoblade ends with the protagonists slaying the incarnation of one of the two titans they had lived on since the beginning of their race, and who had wiped out said race countless times to prevent them from becoming too advanced. Said incarnation also happened to be the originator of that world after first existing in our universe.
Chzo Mythos. Trilby kicks the apparently invulnerable Tall Man in the face.
Crusader Kings 2 introduces an event chain modeled roughly after "The Call of Cthulhu" in an expansion appropriately named "The Old Gods" (focusing on Viking and Pagan rulers). Yes, the player does have the ability to ram Cthulhu with a dragonboat.
The goal of the World Builder game Mormonoids from the Deep is to eliminate the Eldritch Abomination Yog Sogsmith with a suitcase nuke.
Terraria has bosses that are based and named after godlike entities and Cthulu. "Eye of Cthulu", "Brain of Cthulu" after the introduction of the Crimson, and the "Eater of Worlds" all can be punched out. And then there's the Hard-Mode versions...
Bravely Default has this in the Bigger Bad of the game, Lord Ouroboros. All throughout the game, you've been having to restore the crystals as told by Airy. Every time you went through the Holy Pillar, you end up in a parallel world. Once you've restored the crystals in the final world, Airy reveals her true colors and you fight her. You follow her to the Dark Aurora where you fight her One-Winged Angel form until she's killed by Ouroboros who plans to use all the worlds that many other versions of the heroes have linked together so he can get to the Celestial Realm and cause havoc. Throughout the fight, he destroys at least 6 of those worlds, making you just about ready to surrender. It's when the many other worlds fight back and sever his connection that you're fully able to punch this Cthulhu out for good!
Magicka has the player(s) take on an otherworldly being posessing a powerful mage, and winning. For even more adherance to this trope, the DLC pack The Stars are Left has the final boss being Cthulhu itself.
Ys This is what the hero of the series, Adol Christin, does as a day job. He literally goes on adventures and most of the time ends up beating local dieties and Eldritch Abominations armed with just a sword.
In Justice League Heroes: The Flash, if The Flash runs out of health while using his Super SpeedBullet Time mode, the Black Flash (the Grim Reaper to speedsters in the DCU) will appear to take you away. However, you can beat him up and keep fighting with low health. This is rather downplayed, though, as beating him up only stops him for the time being, and every time you do this without getting killed off, he will be much harder to beat.