In addition to Cthulhu Mythos beings, several Canon Foreigners originated from this game, including Arwassa, Baoht Z'uqqa-Mogg and groups of lesser Outer Gods.
There's a board game based on Call of Cthulhu by Fantasy Flight called Arkham Horror which has tokens for hit points, knowledge of other worlds, and (you guessed it) sanity. Every turn, there's a high chance of a gate opening to another universe, and as more gates open, more monsters come flooding through... and as the game progresses, the Doom Count slowly rises. If it gets high enough, the Ancient One (Cthulhu or one of his cousins) appears and the players have to battle it. (Each Eldritch Abomination has special powers — Azathoth's power is "if summoned, the game is over. Azathoth destroys the world.")
The CCG based on Call of Cthulhu (also by Fantasy Flight) has loads as well, although it's actually possible to see a game played in which they don't appear. Just not likely. (Sanity is too valuable as an attack vector.)
Cthulhu Tech. An RPG set about 80 years in the future after the Mi-go (or rather, Migou) have attacked Earth and the Great Old Ones are stirring. It combines H. P. Lovecraft with Neon Genesis Evangelion (what with the gigantic biological weapons called Engels that pilots mentally sync to and ride in their spines). It also throws Guyver into the mix, with abominable Expies of Guyvers and Zoanoids (you can actually play the former).
Balor, the god of darkness. A humanoid being, but of such immense size and power that he can rampage across the world unstoppably. It's a good thing that he's entombed in magical ice. His cultists, the Darkness Elementalists, are granted some of the best elemental spells.
Dungeons & Dragons has whole races of Eldritch Abominations; from 3rd edition onwards, they have been increasingly linked with the Far Realm, an impossibly vast, incomprehensible place far beyond the cosmology of most D&D settings. A 3.5 sourcebook, Lords of Madness, gave greater detail to the "Aberration" creature type, which is mainly used for such creatures (many of the weirder/most horrible Outsider-type creatures also count).
One of the various backstories of Asmodeus, the Lord of Nessus and King of Hell, is that he is actually one of these. What others see when dealing with him is actually an advanced illusion. Asmodeus' real body is that of a titanic, miles long serpentine creature who is still injured from being thrown into hell. Because he was some sort of primordial entity who predated the Gods and who created the Nine Hells when the Gods threw him into them.
The Epic Level Handbook for 3rd edition brought us the Abominations: malformed offspring of deities which desired to destroy all reality. Among the most horrific of them are the Atropal, which are the undead remains of stillborn godlings.
Neth, The Plane That Lives. A whole freaking demiplane that is ALIVE, introduced in The Manual of The Planes. It qualifies as both an Eldritch Abomination and an Eldritch Location. The Far Realm suggests that it contains creatures possibly just as large or maybe even larger, leading to the idea that Neth is one such native of the Far Realm that just so happens to have a portal to the Astral Plane inside itself. It learns by absorbing the denizens of other Planes that visit it.
4e suggests that aboleths aren't even intelligent, thinking creatures; rather, everything they do is the result of a guiding, species wide instinct that is unfathomable by mortals.
While 3.5e and backwards states that aboleths are intelligent and thinking beings, but operate on concepts entirely beyond mortal comprehension; their intelligence is described as a vast and endless ocean, while that of a regular human is but a drop of water. See Blue and Orange Morality, or Lords of Madness.
Aboleths have enough parallels to abominations of the Cthulhu Mythos that the question was directly addressed in the Lords of Madness sourcebook:
Readers will notice a thematic resemblance between the aboleths, the Elder Evils, and various creatures or beings found in the stories of H. P. Lovecraft. This is, of course, completely intentional.
Speaking of Eberron, there's also the Quori, horrifying monstrosities from the plane of dreams with very strong Psychic Powers (usually of the Mind Control or Mind Rape varieties) and the ability to possess mortals; they've already conquered/subverted almost a continent and would really like to take over the rest...
One of the last 3.5 books Wizards released is called "Elder Evils", which features a guide of how to create your own eldritch abomination, as well as several examples of Big Bad Eldritch Abominations, including Ragnorra, the Mook MakerSpace Whale with an Evilutionary Biologist streak; Pandorym, the living Forgotten Superweapon with a personality you don't want anywhere near a Forgotten Superweapon; Atropus, the undead planetoid (who is the quasi-sentient remains of the thing that birthed the universe); Kyuss, The Worm That Walks (that's his actual title); and the Hulks of Zoretha. It also updates/reimagines one of D&D's earliest published examples of this trope: Zargon, a tentacled aberration revered by a fanatical drug-cult in B4: The Lost City.
4th Edition has the Primordials — a primeval race of elementals who created the universe and are powerful enough to destroy gods. They would like nothing more than to destroy said creation, since as their nature are as elementals dictate, they wish to continue an endless cycle of death and rebirth. Most mortals are perfectly fine with the world as it is now, especially since said death and rebirth would include them.
4E gives Warlocks the Star Pact power source, which involves beseeching strange otherworldly creatures that lurk behind specific stars for power. A lot of fluff text suggests that they become a little unhinged. Furthermore, a Dragon Magazine supplement includes an Epic Destiny where you become one of these strange otherworldly entities. It also describes the aforementioned stars and notes their "unnatural" qualities, particularly one that you're better off not looking at for long.
The stars themselves are Eldritch Abominations in 4th edition. And some of them have the ability to create avatars of their power, to the point where even black holes can create such avatars. And at least one of those stars is good; Ulban the Messenger is a mostly benevolent comet god who wants to change the future, but his Star Spawn was featured in the Monster Manual Three, and oh looky, it's evil aligned.
While it mostly deals with Gothic horror, the Ravenloft campaign setting features an eldritch abomination in the form of Gwydion the Shadow-Fiend, Darklord of the Shadow Rift. He became trapped between realities when a planar gate collapsed on him, and really, really wants out. His full appearance is unknown, but what has been seen causes even The Fair Folk to go mad.
The Dark Powers, the force(s) that created Ravenloft itself, since their actual nature, methods, and motives are entirely unfathomable. As well, the Nightmare Court could qualify.
Regular old fiends (demons, etc.) were described in eldritch abomination terms in Van Richten's Guide to Fiends for this setting. It didn't seem inappropriate. Horrifying creatures of great power and alien minds from other realities...
Many of the Cthulhu Mythos deities (such as Cthulhu himself) have entries in the 1st edition Deities & Demigods supplement — and the way 1st edition rules worked, a high enough leveled player character could, in fact, punch them to death.
Basic D&D was no stranger to Eldritch Abominations. Aside from the Nightmare creatures (like the Diaboli and the Malphera), whose physiology was utterly alien and horrific to humanity, there were also the creatures from the Vortex, a place beyond all dimensions and planes of existence, who could cause inexplicable phenomenons with their mere presence. Even the Immortals are afraid of such things.
Dread Tharizdun, a monstrosity that threatens all of existence and that the rest of the gods were forced to cooperate to imprison. Since 3E, Dread Tharizdun has evolved to become a more general Abomination for the whole D&D cosmology.
An entity that actually exists on Oerth itself is the Mother, a bizarre entity served by a colony of degenerate and inbred humans who found it while they fled the destruction of their old empire. Physically, the Mother looks like a large mass of disgusting white ooze that slithers across the walls, floor, and ceiling of the caverns it inhabits, with the ability to drain the life out of anything it makes physical contact with. Unlike the other examples, it's possible for the Player Characters to actually punch the Mother out, as it's mentioned in one of the adventure ideas provided by Gary Gygax in the original 1983 Greyhawk boxed set.
The Qlippoth in the Scarred Lands setting, created third-party company (a White Wolf subsidiary, unsurprisingly) are Obyrith with the Serial Numbers Filed Off (or rather the reverse; see the Obyrith entry above), and cosmology-wise, the Abyss is a cancerous sore that's wrapped itself around reality. And the qlippoth may just originate from whatever is beyond it...
The Far Realms equivalent, called the Dark Tapestry, isn't very far, relatively speaking - it's actually The Void Between The Stars, and to top it off, it's the domain of Lovecraftian entities, Azathoth and Yog-Sothoth included.
The D20 setting Dragon Mech has the lunar gods, mysterious entities from the rapidly-descending moon. There are three main ones: Andakakilogitat, lunar god of dragons, a squirming mass of dragon parts; Erefiviviasta, lunar goddess of flightnote "goddess" because there are slightly more female characteristics than male ones, who is not described; and Seroficitacit, god of change, which is a perpetually mutating and somewhat insane mass of flesh.
In the world of Earth Dawn, the cyclical ebb and flow of magic periodically allows Horrors to slip from their own dimension into the world and devour anything that moves. If you're lucky, they will devour your body before they start on the good stuff. Luckily for the world, magic energies are on the decline, so the survivors the last cataclysm the Horrors caused have just to outlast their ability to keep existing in our world for a generation or two before they're all gone.
Eclipse Phase. Encountering any alien life triggers a stress check, and the only canon sapient species that transhumanity has contacted resemble giant slime molds. And then there's the Seed AI that can potentially achieve god-like intelligence, and the effects of some strains of the Exsurgent virus are not pretty.
Warning, GM only info ahead: the ETI, a Kardashev III or maybe IV entity that created the Exsurgent Virus. Described as being eons old and capable of megascale engineering with an understanding of physics, matter, energy, and universal laws that makes all of transhuman knowledge seem insignificant. And for some reason, it has seeded the galaxy with probes that infect near-singularity intelligences with civilization destroying viruses.
The Primordials came out of said Primordial Chaos and built Creation, with all its gods to take care of it, so that they had time to smoke magical crack. Their minds are so vast that they're divided between entire hierarchies of multiple souls, each of which has a mind of its own and multiple lesser souls with minds of their own.
Most of the Primordials that didn't get killed are now the Yozi, demon princes who have had their very beings and souls turned inside out and who live in the broken body of their leader. They wish to turn Creation into Hell as part of a rather demented plan to escape their prison by expanding it.
The Neverborn are dead Primordials that you have to meet face to architecture. Killing them broke the universe and shat the entire Underworld into being.
Autochthon, a living non-Yozi Primordial, is a giant hollow machine-deity approximately the size of a planet, mostly made of steampunk (and he's a good guy. Sort of.)
The three kinds of Primordial Exalted — Alchemicals, Infernals, and Abyssals — are gradually evolving into something closer to their patrons. Alchemicals gradually turn into cities, but the others have only existed about three years and, as such, have had nowhere near enough time to turn into... whatever it is they end up becoming.
Return of the Scarlet Empress revealed Yozi charms which define the ability of Primordials to exist in their worldform joutennote Technically, all of a Primordial's jouten are defined by charms (as are all of their capabilities and personality aspects). The most accurate way to describe a Primordial is as a sentient collection of charms built around a central theme. Which a Green Sun Prince can learn. Which means that every Green Sun Prince is actually an infant Primordial.
To up the fun, PDF supplement The Broken-Winged Crane gives the Green Sun Princes another path to transcendence, the Heresy charms. Instead of turning yourself into a world, you gain the ability to create worlds within yourself.
Once the Exaltation shard becomes redundant, it is released to be implanted in another Infernal...
In addition, there are also the Fair Folk. The ones that aren't pretending to be something human-shaped for fun are most easily understood as formless living stories who either want to return Creation to the primordial Wyld it used to be or just look at Creation until they get bored and wander off, but ALL of them like to eat the dreams and souls of whatever mortals they can catch.
Fading Suns has the VoidKrakens, who dwell in interstellar space and are never actually physically described. The only sign of their existence is the frequent loss of ships that don't use the Jumpgate system and instead rely on conventional, non-FTL propulsion (such as First Republic generation ships), which sometimes arrive at their (long since settled, due to Jumpgates) destination with ruptured hulls and gigantic sucker marks on them, as well as distress calls mentioning unimaginable, horrific things before being cut off in mid-sentence. The alien races of the setting seem to have had trouble with the Void Krakens as well in the past. The good thing? Apparently the beings cannot enter star systems - it's theoretized in-universe that either the Jumpgates or the stars themselves repel them. The bad thing, which incidentally lends credence to the second theory? Since the fading suns phenomenon began, Void Kraken attacks have again begun after millenia of inactivity. And not only begun, but increased exponentially...
GURPS: Fantasy treats Tiamut as this, giving stats for a minor avatar of hers that, while not particularly odd looking (it's an enormous dragon with four eyes), can still cause terror from just looking at it. Said avatar automatically regenerates every year, making the effort of trying to kill it futile. To get rid of it permanently, you'd have to track down and kill the real Tiamut... who is half the size of the universe (about 2.24* 10^18 Hit Points), so good luck with that. There's even a Lovecraft quote after the stat block.
GURPS has a few more from different settings and splatbooks: GURPS: Cabal, with its cosmology based on the qabbalah's Sephirot, has the creatures of Qlipoth and its Ur-Lords; Creatures of the Night has the godlike Betweeners, the force called "the darksome", which is responsible for the creation of the literal organ-farmer Darklings, and many of the non-undead creatures described; a few licenced settings (like Cthulhupunk and The War Against the Chtorr) have their own native abominations; and Infinite Worlds, the meta-setting that ties The Multiverse together, not only makes all the previous settings inter-accessible, but also has at least one world (Taft-7) where humanity never evolved in the first place because of Great Old One (or similar) influence 50 million years back - and although they're long gone, they left enough "Fun Stuff" behind (and the risk of attracting their attention is great enough) for the agencies overseeing interdimensional travel to quarantine the world from any travel there whatever the reason.
While our nature in Kult allows us to kick most super beings with ease once awakened, the Forgotten Gods are different stories. These beings represent principles incomprehensible to humanity and are powerful enough that they do not even care about the plans of the Demiurge or Astaroth.
For those who don't play MtG, a brief explanation: the deck, generally consisting of 60 cards, represents the player's spell reserve and memory remaining. So, effectively, everytime the Nemesis of Reason even looks at you funny, you lose one sixth of your mind. No questions. And Marit Lage? She is 20 times as strong and resistant as one of the heroes who defeated the Empress of Fae in one of the more recent sets, gameplay wise. The player's role is that of a Planeswalker, one of the most powerful kinds of beings in existence. The starting life total is sufficient to survive multiple attacks from Leviathans, Kraken, or Ancient Dragons. Marit Lage will kill you in one hit.
The fluff for the Zendikar block strongly hints at the existence of an entire race of abominations called the Eldrazi, all of which got locked away inside planets by a coalition of aforementioned planeswalkers. The name of the final set in that block? Rise of the Eldrazi. The (comparatively) good news is that this is probably localized for now to Zendikar, and (hopefully) will be stilled there by Jace and/or Chandra. Still, there's something very unsettling about them. In M:tG, everything except lands and artifacts have at least one out of the five colors of mana associated with them; those mana colors define what aspects of reality they are most attuned to. Lands, meanwhile, almost always supply mana, and when colorless mana is supplied, that usually means mana too raw to have a particular slant; think of "colorless" as actually meaning "no particular attunement to a specific aspect of existence". The Eldrazi in question? They don't have a color. And no, they're not artifacts (the only type of colorless spell card until then). They're alien to the structure of the known multiverse. And if that Annihilator keyword is anything to go by, wherever they go, a bit of the multiverse there gets destroyed. And to think that they were once worshipped as the main gods of Zendikar...
Now that the whole set has been revealed and released, there are THREE Mythic Rare Legendary Eldrazi: Kozilek, Butcher of Truth; Emrakul, the Aeons Torn; and Ulamog, the Infinite Gyre. These can't be killed permanently unless you exile them, since as soon as they hit your graveyard from anywhere, you shuffle your entire graveyard into your deck. There are six more non-Legendary Eldrazi, the smallest of which is a 7/7 and is COMMON. Of these six, 2 are common, 2 are uncommon, and 2 are rare. All of them have the Annihilator ability. Plus, there are several cards that create Eldrazi Spawn (small creatures that can be sacrificed for mana to help cast the big guys). And there are four non-creature colorless Eldrazi spells with considerable power. The mythic rare All is Dustdestroys everything that has a color and the rare Eldrazi Conscriptionturns any creature into an extremely powerful Eldrazi.
The Eldrazi are so alien that they didn't originally even have physical forms. The only reason they do now is because the spirit dragon Ugin, one of the three planeswalkers who imprisoned them in Zendikar, pumped them full of his colorless Ghostfire to trap them in bodies that could be imprisoned by the other two planeswalkers.
If you're curious what they look like: the picture on the main page is Emrakul.
There was the original abomination if you go WAAAAAY back to the Legends expansion. The art says it all.
The "Horror" creature type was actually used as a grab-bag for a blend of vat-grown monsters, demons, experiments Gone Horribly Wrong (or worse), and other creatures that shouldn't have been for various reasons. That said, many are indeed unbelievably horrific things that will burn your sanity.
The oldwalkers themselves could count, their physical forms being but projections of will, making them essentially immortal and able to take on any form they desired, as well as being nigh-omnipotent and able to escape planes and walk through the blind eternities, the place between planes, that is a vast realm composed of Aether and being contradictory and completely alien, which none but planeswalkers can survive.
They also tended to come to regard mortal lives as having little to no value.
The Lords of Cthul from Monsterpocalypse are the Cthulhu-esque, Godzilla-sized avatars of powerful extradimensional monsters... who get bodyslammed regularly.
In the Tabletop GameMonsters And Other Childish Things, one of the types of monsters used in its dark and twisted take on Mons are Eldritch Abominations. The non-statted sample monster Dewdrop is an Eldritch Abomination take on a unicorn, while one of the statted sample monsters is a Lovecraftian monstrosity merged with a teddy bear named Yog-So`Soft. Both these and the more "normal" monsters tend to cause bouts of panic and madness in people who see them as well, further adding to it. There are also a few non-Mon antagonists that are also abominations.
Well, though the RPG of Mortasheen isn't out yet, there are three creatures in the setting so powerful they might as well be these. Called The Destroyers, these unfathomably powerful weapons are as follows.
There is Hestermoan, a horrible Nuckleavee-esque monstrosity created "as an instrument of genocide against a civilization, and so effective that their very name remains unrecoverable". It is every variant of Plague Master rolled into one horrible monstrosity, including a Hate Plague to boot.
The "honorary" Destroyer, the Necromon. Originally just The Symbiote, a unique mutation caused it to grow in size and intellect until it became a Physical God with control over its smaller brethren, all of which serve as Amplifier Artifacts which also were the basis for an entire genus of monsters. It's friendly, but it says something that the attempted replication of it is a capital crime in Mortasheen, on the basis of what happens. The same people who banned this created the Destroyers, so something that scares them must be really bad.
Spoofed in the Munchkin Cthulhu stand-alone Munchkin set and its expansion, The Great Cowthulu. It added a new dimension to the game in the form of the players being able to become cultists. And if everyone in the game became a cultist, the game was over as Cthulhu won. Also, one of the monsters featured is the very cute Chibithulu. Cthulhu also shows up as a monster in the original Munchkin game (based on Dungeons and Dragons).
The Unspeakable One from the Freedom City Mutants & Masterminds setting. (It also provides Golden Age stats for an eldritch entity, although that barely qualifies - it may look like Cthulhu, but it doesn't drive you mad simply from looking at it.)
In White Wolf's Old World of Darkness, cosmic horror story is not the central theme of the game, but the authors love to incorporate Eldritch Abominations from beyond time and space into the setting, whose presence corrupts souls, drives people insane, or warps reality. To break it down a little:
Changeling: The Dreaming gives us the Fomorians, ancient, formless primordials and lords over winter and dark dreams. They were banished to the depths of the Dreaming by the Tuatha de Danaan, but as Winter approaches, they've started to make their way back...
Mage: The Ascension has some of the patrons of the Nephandi. The Malfeans worship the Wyrm (see above), while the K'llasshaa worship the Outer Lords, broken alien beings who feed on negative emotion and who were supposedly the lords and masters of the world in its pre-history.
In Vampire: The Masquerade, most of the Antediluvians are still quite humanoid - in appearance, at least. But then you've got people like Ennoia (the Gangrel Antediluvian, a mass of animalistic features who is believed to have melded with the earth itself, rocked to sleep by its rotations like a babe in the cradle), Malkav (the Malkavian Antediluvian, willingly diablerized by his clan, existing in their head as a madness-linked Hive Mind, and sometimes appearing in forms such as twelve identical little girls), Lasombra (believed destroyed, but instead he became one with the lightless Abyss that helps power Obtenebration) and Tzimisce (a gigantic mass of sculpted flesh).
Which, in the case of V:TM, makes it only scarier, seeing as the central theme of the game is how a human is transformed into a monster and to what extent this transformation can go (and how it can be fought). Usually, the transformation is psychological - holding on to the last shreds of humanity is a necessity for a player character (unless he/she chooses a vampiric Path). But, with the Tzimisce, it is also physical, and willingly self-inflicted. The scary thing about powerful Tzimisce, especially the Antediluvian itself, is that they were human once, and are Eldritch Abominations now.
Werewolf: The Apocalypse gives us the Wyrm, originally one-third of the primal forces of existence and the blessed end of all things until it got caught up in the webs of the Weaver, at which point it turned its goals towards corruption and destruction in an attempt to weaken its bonds. Most of its servants are either subjected to eternal decay or driven mad by its wisdom.
The Weaver itself is no slacker in this department either, though its particular set of strange and alien activities is actually more alien than the Wyrm, and thus less likely to single out the players for destruction.
Wraith: The Oblivion has the Neverborn, forever-dead, eternally-dreaming lords of Oblivion whose scattered thoughts serve to drive and guide the Spectres. Orpheus gives us Grandmother, the thing that created the Neverborn.
The True Fae of Changeling: The Lost skirt the line between The Fair Folk and this, especially when taking into account the rules in the Equinox Road sourcebook. In addition to the traditional inhuman beauties and horned hunters, you might face a Fae that appears as a pool of sentient darkness, a squamous, be-tentacled thing, an entire tribe of ogrish monsters, or the whole Arcadian realm itself.
In addition to mentioning the below Chthonians, Geist: The Sin-Eaters supplement Book of the Dead introduces the Leviathan, the Kerberos of the Ocean of Fragments, who pretty well embodies this trope. It's an impossibly vast sea creature of some sort — it's assumed to be a cephalopod, but that's just because it has tentacles; it's too big for anyone to ever see enough of it to make out its true form. Every human in the world has had nightmares of it lurking beneath them in an endless ocean, even if they've forgotten them. It cannot be killed or placated, any more than the tide or any other force of nature, and stats are provided solely for the purposes of escaping it or inconveniencing it enough to drive it off temporarily. Fortunately, it's rarely seen — to the point that most people think the Dead Dominion's only other notable inhabitant, the Admiral, is actually its Kerberos.
With the release of the God-Machine Chronicle, we now have the titular God-Machine. Let's put it this way: Literally the first quote in the book is Clark's Third Law, and it's implied to have created the concept of technology on Earth so humans could create spare parts for it. Bonus points for being the most classically Lovecraftian being in all of both Worlds of Darkness: It isn't malevolent, it isn't cruel, it isn't even mindlessly destructive. It's just completely apathetic towards human existence.
BIG Hunter: The Vigil spoiler: The Cheiron Group is run by ten of them, with illusions of human beings to let them interact with people. It's the Storyteller's choice whether they're working to defend our world or are planning to exploit it for everything we've got.
Abyssal entities from Mage: The Awakening come from what could best be described as an "anti-universe," a world that lives by rules wholly antithetical to those of Earth. Truly, however, the most horrifying thing about Abyssal entities is that the idea that beings of the Abyss always take such predictable — horrifying and maddening, but predictable — forms as "monstrous, unclean abomination" is actually a comfortable lie that Mages tell themselves to hide from the fact that the Abyss is, in fact, in no way as banal and quantifiable as that.
An Abyssal entity that's been known to sell a lot of prospective players on the setting is the Prince of 100,000 Leaves, a demon made of living anti-history whose first summoning rewrote history and spawned a cannibal cult that eats its victims out of history in an attempt to bring the world in line with the Prince's native timeline.
Oh yeah, and Imperial Mysteries has the reason for the strange predictability: each and every Abyssal being is actually a resident and part of a Greater Abyssal Entity. You know what those are? Semisentient stillborn universes. The Prince is explicitly stated to be an example of one, with all his manifestations being him trying to replace all of reality. Now think: what kinds of beings gave birth to everything else in Intruders, since they aren't part of the Prince...?
The SourcebookSummoners includes some other examples, such as the Chthonians of the Underworld (known as the "neverborn" since they exist in the realm of the dead, but cannot be reliably said to have ever been alive) and certain Supernal beings.
The sourcebook Second Sight has a pretty good chapter on building your own abomination, a Misanthrope Supreme or Fallen Hero to serve as their high priest, and a cult to worship them. The creation example is a being of dissonant sound. (Although one suggested weakness for this being — music of unity — seemed uncannily reminiscent of Ghostbusters 2.)
Genius: The Transgression has the Cold Ones, entities living at the end of time, who'd like to go back and experience things like heat and movement.
Nobilis has three main types. First, the True Gods - some of the earliest gods to come into being, to be found below the world in an enormous mass of tentacles and weirdness, simultaneously fighting and mating with each other. Next, the Excrucians, beings of not-being from outside reality who aim to destroy the universe, and finally, the Actuals, the precursors to the True Gods - the movement like life, before it learned to live. The Actuals are vital to the existence of reality - but if one is summoned into the world, it will consume everything in a futile attempt to attain self-awareness if it isn't stopped. The True Gods, on the other hand, could quite possibly be the guys who empower the PCs.
Spoofed in Pokethulhu. Yes, there are hideous, evil, non-Euclidean critters. But you can tame them and use them as Mons (and they still drive you to insanity).
Rifts has a lot of these monstrosities in its ranks, and several different kinds are present on Earth. The first two world books alone (on Atlantis and South America) have the Splurgoth and the Vampire Intelligences. Both are functionally mountain-sized eyeballs with mouths and tentacles, but the Vampire Intelligences are arguably more dangerous; they are the ultimate source of all vampires throughout the Megaverse, and cannot even manifest themselves unless a sufficient number of vampires are already existing first.
In Glorantha (as seen in RuneQuest and other sources), Chaos is like this. One major empire has an enslaved Chaos god/demon/thingy called the Crimson Bat. It's huge, it flies, it is covered with eyes, it glows with unholy energy, and it will eat your soul. It is crimson, and I suppose it's at least as much like a bat as it's like anything else... which isn't much.
The Greater Titans of Scion are beyond mortal ken. They're beyond divine ken. They are so divorced from reality (despite being incarnations of its primal concepts) that they had to divide their power among Avatars just to have a clue what they were doing. Each one is its own internal world. Worst of the lot, though, is Hundun, the Titan of Chaos. It alone of the Titans couldn't be bound, for doing so requires definition - and Hundun cannot be defined. An easy way to enter Hundun is to have a God become the Void, the living embodiment of chaotic... and then jump in.
The Star Wars RPG has the DarkStryder, a self-aware supercomputer created by a Precursor-type race that has created several species of its own and looks like THIS◊ and the Mnggal-Mnggal, a sentient fluid adept at possessing bodies so horrible that even the Celestials (a Precursor race even more mysterious than the DarkStryder's creators and believed to be nearly omnipotent) didn't want anything to do with it and sealed it away. Word of God from the creator of the latter abomination says it's supposed to be the same type of being as fellow Star Wars abomination Waru.
Parodied in Toon with the "Crawl of Catchooloo" setting, full of Slurping Horrors that can drive a typical Toon character sane.
Unknown Armies deliberately subverts this trope, at least in a way. What's scary about the universe isn't that it's so alien and vast and inhospitable to humans. What's truly scary is thatYou Did It.
Warhammer and Warhammer 40,000 both have the Chaos gods. Residing in the deepest layers of the warp, composed of every sapient thought and emotion, they personify things like rage, scheming, despair and lust, but also things like honour, hope, resilience and love. They are so powerful and so incomprehensibly vast that they are utterly incapable of influencing anything outside of the warp, requiring their daemon hordes (all of whom are both separate individuals and aspects of the respective god) to recruit and kill in the material plane in their name.
Tzeentch deserves special mention, because it is essentially the personification of cause and effect, meaning that as long as some things cause other things, it grows in power and influence. In a setting where all of the gods are intentionally or unintentionally malicious, Tzeentch is extra terrifying because sometimes his gifts DON'T have any kind of catch, and are distributed frequently based on whim and randomness rather than any kind of consistent evil — there is literally no way to know whether you're part of a plan or not, and even if you think you are there's no way to know whether the plan is intended to succeed or fail.
The C'tan of 40K were literally the oldest beings in the universe, creatures of light that wrapped themselves around stars to feed off of them, and operated on a scale so vast they originally had no idea that planets existed, let alone the noisy little things living on them.
While the Tyranids may seem more like a Horde of Alien Locusts, the quintillions upon quintillions of ravenous beasts it unleashes are not actually individual beings, but merely a tiny part of the unimaginably vast single organism that is the Tyranid Hive Mind. Utterly alien and of a near unprecedented power, capable of screwing with psykers and daemons within hundreds of light years of it, even people who have regularly fought and bested the horrors of the warp are terrified of such an implacable force.
The original Warhammer has the Gods of Law, which are arguably more inhuman and, should the unlikely case of their victory occur, will turn the world into a stillborn reality where no change of any sort occurs. This is particularly more true to Alluminas, whose requirements for his worship are extremely bizarre and who can cast a light that makes anything it touches unmoving and unchanging.
In The Whispering Vault, the player characters are all minor Eldritch Abominations who act as a "police force" that apprehends and retrieves other abominations who have illicitly made their way to Earth. Reality is also All Just a Dream cooked up by those abominations who haven't gone rogue.
Worm Zero is a giant, moon-sized thing that looks like it has multiple heads sprouting out of itself, going by its effects, it can erase monsters by assimilating them, implant some hive mind knowledge into its user, or give birth to a worm. Said worms could also qualify, given their origins.
One of Pegasus' signature monsters, Relinquished, could also qualify. Its main gimmick is assimilating an enemy monster into its body, taking on its stats, and using it as a meatshield in the event that it might be destroyed. Even worse than this is Thousand-Eyes Restrict, a Fusion Monster that is summoned using Relinquished as one of the components; it does the same thing that Reliquished does, but also prevents all monsters except itself from attacking (the anime suggests that this happens because all other monsters are paralyzed by fear). On an unrelated note, Thousand-Eyes Restrict is so powerful as a card, it's currently illegal to use for official games.