In the backstory of the game Fading Suns, the meeting between the Vau and the Second Republic (nearly at the highest point of its power and technological advancement) is the conquest of a (unknown to the humans) Vau protectorate. A few days later, a Vau ship appears, destroy every trace of human presence in a matter of minutes, and leaves a message not to fuck with this star system. Of course, humans being what they are, assemble a combat fleet to attack the planet the Vau vessel came from. The only ship to come back had been spared to serve as a warning to the Second Republic.
In the backstory of Planescape, it's mentioned that Sigil's mysterious ruler/protector/overlord, The Lady of Pain, has killed gods in her time...and the confrontations were not the usual, cataclysmic, ground shaking clash of the titans one would expect from a duel between major powers. They were much more of the "angry Lady = dead schmuck" variety. The only entity that has ever so much as slowed her down is Vecna, a millennia old liche and greater god, who was in the process of reshaping the multiverse at the time. Everyone else just dies.
She can appear in Planescape: Torment as a non-standard game over if you cause enough trouble in her city, perma-killing the Nameless One in one shot.
In Exalted, this is almost guaranteed to happen any time a Celestial Exalt goes in against mortals, or even Terrestrial Exalted. It's even possible to curb stomp gods if you have the right build.
'The right build', of course, meaning 'being anything stronger than a regular heroic mortal'. And even then, a heroic mortal with an artifact that allows him to hit dematerialised spirits...
Depends on the god. Lesser river god? Fuck, yeah. One of the higher-ups, i.e. The God of Southern War and Cattle, or the Celestial Incarnae? Not so much.
The card Crushing Attack in Legend of the Five Rings can only be played during a battle if you have more than double the strength of the opposing army. It immediately ends the battle, preventing any actions from your opponent that might have swayed the outcome, purely by overwhelming might.
High-level characters in Dungeons & Dragons can typically be counted on to wipe the floor with low-level characters in a straight-up fight. This is especially true if spellcasters are involved, as many high-level spellcasters have spells that can instakill characters below a certain HD level with no saving throw.
Spycraft, and later D&D 4th edition, had separate NPC types for "minions" or "standard" characters and "special characters". The latter have hit points like the player characters, but the former die with a single successful attack. Needless to say, a combat encounter designed primarily around standard/minion characters tends to be this until players reach the 'boss'.
The Witcher: Game of Imagination has this stance as default toward random mooks and similar enemies and mechanics that actively support that. Characters with Poor or Average skills or stats, short of pure luck, stand almost no chance against those with Good or Excellent parameters, not to mention Legendary. Other than that, there are few in and out of universe examples that can turn really, really nasty:
Being ambushed by dryads is considered this both in and out of universe. In-universe, they are race of bow-totting Cold Snipers and Stealth Experts, so when they attack, their enemies usually don't even know what hit them. In gameplay terms, due to all the things they get for being a dryad is enough to make them scary - and they can obviously have better skills than the starting ones. Surprise attacks cause all the defenses, regardless of how high they are, being reduced to 1. Even the worst dryad archer can auto-hit anything with defences of 3. This allows them to take a really good aim, adding extra modifiers to damage. Or just go directly for vital organs. Or, which is the worst that can happen, simply pour Rain of Arrows. A few small squads of dryads can slaughter entire batallion as if nothing. Worst part? If a character somehow survives the first round, dryads still retain their stealth bonus.
To a lesser degree, all kinds of encounters involving rangers play like this. Defense against projectiles only scales with Agility (everything else scales with Agility/Will and skills). This can be somewhat mitingated with shields, as they provide decent defense against projectiles (up to +3). But if rangers shoot from hidden position, they still have advantage of lowering defenses of their target(s) to 1, allowing to add further modifiers without fear of missing the shot.
Ever heard how Bears Are Bad News? A single bear has more Vitality than most of predators and magical monsters, so it can shrug off some of the most powerful attacks in the game and keep going. It can attack three times per turn, and all of those attacks must concern the same target. And while the rolls for damage already look vicious (a whooping 7d6 in total), the actual scary part is that each attack comes with 12 of fixed damage, giving 36 of damage, regardless of rolls. And maximum Vitality of a PC is 35. Oh, and for obvious reasons, bears are pretty common.
High vampires are quick and strong enough to kill in a single round at least 3 well-trained and equipped characters. They combine lighting speed with staggering resistance to absolutely everything - not even fire, a standard weakness of all tough enemies, can harm them. And if they will be somehow harmed, they can regenerate up to 2d6 damage per round. To put that into perspective, a decent melee character can deal about d6+9 with really, really good roll.
A single dragon can take down a small army with ease. Being a huge, flying and fire-breathing lizard with natural armour capable of shrugging most of conventional weapons has a lot to do with this.
Normally what happens when a Planetary Defence Force goes up against anybody. Think the Imperial Guard, except they lack the one thing that make the Guard a force to be reckoned with: sheer quantity. Happens depressingly often with the Imperial Guard as well, especially in stories where the protagonists areSpace Marines. When Tyranids appear in fluff, they're usually the ones delivering the curb-stomp.
In the 30K version of the game, the Space Wolves Primarch Leman Russ is an absolute close combat monster who'll quickly kill anything that gets within arm's reach of him. Even Horus can't hold out for long against him. The Space Wolves themselves were known during the Great Crusade as "The Rout" because they were the ones the Emperor sent when he really wanted an enemy crushed. Exhibit A: The Interex.
If a Chaos warband ever manages to summon a Bloodthirster then usually the remainder of the conflict will be decided in their favour very quickly.
For specific examples:
Horus vs. Ollanius Pius. The former was the strongest and most skilled of a bunch of demi-gods before the Chaos Gods used him as a receptacle for power. The latter was a standard Guardsman, the same as the ones who die in droves against the alien and mutant every day. Pius died standing, if only because his skin hit the far wall before the rest of him hit the ground.
Primarch Sanguinius vs. Ka'Bhanda. After a short battle, the greatest of Khorne's daemon lords was sent back to the Warp with no wings, a broken back and a serious case of butthurt.
The Battle of the Blood Nebula. The Imperium, finally having enough of the Eldar, decides to root them out at the source and destroy a Craftworld. Unfortunately, the one they chose was Biel-tan. Result: an entire Imperial sector fleet annihilated, with Biel-tan taking minimal loss. The defeat was so utterly crushing that it caused the Imperium to drop the whole "exterminate the Eldar" idea and simply deal with them as they crop up, although it didn't stop the Invaders Space Marines from delivering their own curb-stomp on Craftworld Idrahae later. In a three-fer stomping, the survivors of Idrahae went to Craftworld Alaitoc for help, and Alaitoc sent a force to the Invaders' homeworld; as a result, the Invaders were forced to become a fleet-based chapter.
The Doom of Malan'tai. An entire Eldar Craftworld lost to a lone Tyranid zoanthrope. Ok, admittedly, the stomping happened after it ate all of the soul energy of the Craftworld's Infinity Circuit, but still, not one of the Eldar's finer moments.
A similar even occured in the days of the Great Crusade, where humanity encountered a species that no longer used open warfare, but had armies fight it out in vast arenas to determine the winner. The Imperial fleet notices the arenas half-full of alien warriors looking expectantly at the sky... Orbital bombardment ensued.
Pretty much the whole schtick of the Legion of the Damned is jumping into battles where the Imperium is on the receiving end of a stomping, and turning the tables. The Space Wolves are also pretty famous in-universe for dolling these out.
The so-called Dominion of Fire. Primarch Angron as a daemon prince of Khorne comes out of the Eye of Terror with 50,000 Khorne Berserkers at his back and ravages seventy sectors over two hundred years of bloodshed. It takes the Imperium four Space Marine chapters, two Titan legions and more than thirty Imperial Guard regiments to retake everything. Later on, Angron comes back on Armaggeddon and the Imperium, taking no chances this time, deploys over one hundred Grey Knight Terminators (super-elite psychic Space Marines specially trained to fight daemons) to cast him back into the Warp. They succeeded, but nearly all of them died.
The Singularity System models vehicle-scale and personal-scale combat with the same system. Unsurprisingly, cross-scale combats are usually Curb Stomp Battles in favor of the vehicular-scale combatants. This is not always the case, though, especially when Powered Armor come into play.
Any time a traditionally equipped Martian army gets into a scrap with a modern force in Rocket Age. The Deutsche Marskorps and their war-walkers in particular are the masters of this.
In RuneQuest, it's established that attacking the dragonewt home city and destroying their eggs - the focus of their repeated reincarnation - is completely off limits. The reason lies in the last time it was tried: The true dragons got very, very upset and the resulting Dragonkill Wars weren't so named because of anything the dragons suffered. Ever since, it has been understood that battling individual dragonewts is allowed, but attempted genocide is a giant no-no.
As per other games above, pretty much guaranteed in Anima: Beyond Fantasy if low-level characters fight high-level ones. To give some scale, here someone of around level 3 is considered, to give a comparison, the equivalent of an elite soldier (think of Rambo) and those of around level 6 equivalent to people who in Real Life are just a-few-in-all-history. Level 8 characters and higher are said to be able to single-handedly destroy an enemy army, and it just continues going up from there... until someone finds that the game's most powerful entities (Beryls, the Shajads, C'iel, and Gaira) could kill the highest-level character someone could think of with just the equivalent of winking an eye.