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Alan Wakeimplies that the Dark Presence is one of these; trapped under Cauldron Lake and waiting for someone to set it free... It has a human Avatar controlled by the Dark Presence which is implied to be the avatar of an even worse thing.
In Amnesia: The Dark Descent, you are being followed by these "things" or "shadows" as you explore the castle. You have no weapons/defense other than hiding either, so there is a sense of hopelessness. While their appearance is a blurry/melted shambling humanoid, staring at them for more than a few seconds will cause you to lose sanity (an in game statistic). Worse, those are just mooks. The journal scraps/notes you find hint that the main bad guy "comes from beyond the void" and "warps reality with its presence", which you experience as you progress through the game and parts of the castle are warped into nightmarish versions, with raw flesh coming out of the walls.
Gohma Vlitra and Chakravartin from Asura's Wrath are relatively hard to comprehend, especially when the latter changes into its final form. The extra materials even say that their gender and age are unknown.
In Bayonetta, Jubileus and Queen Sheba are analogous to God and Satan respectively, but the severe Crapsack World means they don't actually care about individuals and are fairly mindless despite their horrendous power. The angels themselves count, specially Iustitia, one of the cardinal virtues, intentionally designed like a mixture of a carnivorous plant with a tentacle monster with creepy cherubic baby faces everywhere because of its moral ambivalence.
The Domz priest in Beyond Good & Evil commands an army of twisted beasts and people corrupted by its influence, able to control all of them with gargantuan psychic powers that render nearly anyone helpless against it. It is only able to be defeated at all because Jade is also an abomiantion.
BlazBlue has The Black Beast, a horrifically powerful monster that appeared about a hundred years before the game's story kicks off, nearly destroyed the world, and turns out to be a fusion of Ragna and Nu-13 trapped in a Stable Time Loop. There's also Arakune, a crazy blob... thingwho is actually a failed attempt to create The Black Beast.
This series' depiction of Dracula is actually closer to this, with a dash of The Antichrist, than to a traditional vampire.
Champions Online has the Kings Of Edom - godlike beings from previous universes with names like "The Heart in Man's Dementia" and "The Muse of lethargy and Despair". They dwell in the Qliphotic, a realm beyond even hell, that has been revealed to be a dying universe. They dwell within a universe, draining it of all energy and life, then take new avatars in the next universe. And our universe is in their sights as their new home.
Lavos from Chrono Trigger — a horror from space that descended to Earth when it was young and slept and ate until it was awakened to destroy it in 1999. In Chrono Cross it merged with Schala and became the Time Devourer, which lurks at the Darkness Beyond Time where cancelled timelines go, growing in power and preparing to destroy universe. We see it in its full hideous glory in the Bonus Dungeon of the DS remake, there known as "Dream Devourer". After you "win," The Battle Didn't Count since it just absorbs a self from another reality where it doesn't die. It's mere presence and feeding on the planet weakened the fabric of spacetime at key moments of history (therefore allowing time travel to be possible, which set up the series of events leading to its demise at the hands of the localMeddling Kids). Even better, Lavos is summonable through occult ritual and is itself a source of magical power. Originally, humanity used the sun as a source of magical power, but the sages of the great magical kingdom of antiquity tapped into Lavos, and apparently, he beat the sun's magic, managing to power a floating continent of mages even before they managed to directly tap into its power. The main characters end up using sun-granted magic to defeat him, so there.
The eponymous being from Chzo Mythos. A pain elemental who absorbed all its rivals, to the point where Chzo became a literal mountain of flesh that took over a sizable portion of the Ethereal Realm. A whole lot of events (that it could plan out ahead of time, thanks to it being in every possible time) and manipulations later, Chzo had a Religion of Evil on his side, a practically invincible right-hand-man, and had all but succeeded in creating the bridge between our realm and the Ethereal Realm... We'd be all boned had everyone not been fooled to the point where they hadn't realized that Chzo would actually die if he crossed over to Earth. He wasn't intending to cross over, anyway — he was actually trying to get a New Prince. And he succeeded. After all the deaths, trauma, and general misery, nobody was expecting Chzo to actually win in the end.
Rularuu, a Planet Eater who was only defeated by banishment to the Shadow Shard, a weird, twisted dimension. His minions are things like giant eyeballs with teeth and giants made of crystal, he commands reflections of the inhabitants of the worlds he's devoured, and you never face him directly — just fragments of his personality, which in and of themselves are ridiculously powerful archvillains (except for the heroic fragment who helps you).
Hamidon, a giant single cell monster that is the largest Giant Monster in the game and leader of the Devouring Earth faction, may count. Though it is implied that he was once a person that became what he is through a combination of science and magic, there are some people that will swear (rightly so) that he is a god. (He was actually referred to as 'a dark god' in a press release, though the writer later admitted they didn't check the facts.) It's recognised in the fluff as arguably the greatest threat to all other life on Earth in a world filled with superbeings, gods, demons, and aliens and is known in-game as the most powerful enemy yet, who you should only try to tackle in 50-character raids. The Praetorian version of Hamidon is even more powerful, having taken over most of the surface of the Earth.
Turns out Santa Claus is one, if you upgrade him enough. Although the fact that the newsfeed keeps referring to him as nice implies that he's Creepy Good.
Copy Kitty has the Bonus Boss, Exgal. Its name cannot be displayed except as bizarre characters, and its life bar is messed up and never goes down. Instead, Boki has to destroy its three puppets. Each time she does so, she can absorb one of their similarly unnameable but extremely powerful abilities. Exgal only goes down when Boki combines all three abilities and... um... well, seemingly summons Azathoth. Whatever actually happened, it was something that crashes the entire training simulation and wasn't even supposed to be possible. Afterward, if you try to view Exgal's data in the enemy list, it corrupts the interface and makes everything unreadable. This was apparently a watered-down version of something Boki will have to fight if she ever completes her training.
Custom Robo on the Gamecube has Rahu, the Big Bad. Originally an intangible force of destruction that annihilated anything it came across and very nearly caused The End of the World as We Know It, it for some reason merged itself with a children's toy (the eponymous Robo). That turned out to be a very stupid move: while Rahu is still pretty powerful, it is also defeatable in that form.
The Dark Souls content in the Prepare to Die edition introduces Manus, Father of the Abyss, who is heavily implied to be the Dark Soul's wielder, the Furtive Pygmy. With this revelation, it might not be too inaccurate to say that anyone who has a Lord Soul has a good chance at becoming one of these.
Dark Souls II has quite a few, from The Rotten, a massive pile of corpses given life that appeared in the trailers, to the Darklurker, an insanely powerful... creature... living in what became of the abyss between the game and it's prequel
The Tyranid campaign of Retribution has the player take orders from one, eventually leading to a Cosmic Horror Storyending. Well, "take orders" in the sense that you receive barely comprehensible flashes of emotions and intent from a galaxy-sized Hive Mind. "psychic beacon... antithesis... presence felt... darkens way... descend... Destroy... must clear way..."
Dead Space 2 has The Marker, while Dead Space 3 has The Moon (and its brethren). It is the Bigger Bad of the entire series, manipulating everyone for centuries through the Markers to restore its full strength.
Many of Cthulhu Mythos' deities appear in Demonbane. Although the Great Old Ones are treated as just powerful monsters, the Outer Gods still play it straight. Unlike in the mythos, most Outer Gods are sealed in compact universes inside the Shining Trapezohedron. But Azathoth still generate countless universes from inside, making it the center of the multiverse (and the destruction of the Shining Trapezohedron will doom everything, for Azathoth will turn the whole multiuniverse into an Eldritch Location once it's free). At least two Outer Gods are free, for neither of them can be sealed. One is Yog-Sothoth (being the embodiment of all time and space) and the other is Nyarlathotep (being the will of the Outer Gods, and since the multiverses come from the thoughts of Azathoth, sealing Nyarlathotep will simply drive it from your universe for a while, then it will re-emerge with another mask in an alternate universe). One of its forms, Clockwork Phantom, is an elaborate version of the Tik-Tok Man in the mythos, being a mechanic abomination that assimilated whole universes into itself.
Baal is just as old as the universe, absurdly powerful, and immortal.
It's implied that the most ridiculously powerful of Disgaeademons start to turn into these. The true Overlord Zenon was becoming a completely inhuman (so to speak) Omnicidal Maniac and had to turn to Reincarnation for a way out.
This is a surprise in Disgaea 3 when you realize that Mao looks a whole lot more like his father than initially implied.
Disgaea 4 has you say hello to Death/Extermination Submersible Combat Organism —aka Desco◊, the cutest widdle eldritch abomination that ever wanted to be the Final Boss. Just because she's moe, doesn't mean she's incapable of turning you into a gibbering mass of fear and insanity, if her attacks◊ are anything to go by.
In Drakengard, The World Is Always Doomed because the gods are not just evil, but also composed entirely of Eldritch Abominations. There are not slithering masses of tentacles that cause insanity by their very sight, but something very morbid. And they're not just restricted to one dimension either! Their very presence in Shinjuku in Ending E causes such horrifying destruction to that world (due to a supernatural disease they brought with them) that humanity is driven to near-extinction, AKA the world of NieR. Which itself has more than its share of abominations as a result. Drakengard 3 reveals that the Grotesquerie Queens were originally the Intoners, beings created by a magical flower. One in particular is revealed to be the goddess of the Cult of the Watchers, deified by her Opposite-Sex Clone after he went mad.
Later games attempted to pass Sithis off as a more traditional god of death, but the backstory reveals that he is a great void, the undying soul of a dead primordial force. Sithis Is Not.
The Daedric Princes are alien beyond human understanding, though they can take any form they like, and so will often take a humanoid form to deal with mortals. (One of them, Hermaeus Mora, doesn't bother with this and resembles a more typical abomination.) They don't share the sense of "good" and "evil" mortals have. How they feel about the mortal races varies from prince to prince; many enjoy being worshiped, some just enjoy toying with mortals' lives for their own amusement, but all of them have demonstrated a willingness to reward mortals they find particularly helpful, loyal, or amusing.
Hermaeus Mora ditches any semblance of sanity in Skyrim and appears as a "Wretched Abyss" — a living dark vortex. In the Dragonborn DLC, he appears in a truly mind shattering form with a seemingly infinite amount of tentacles and eyes.
Alduin, Big Bad of Skyrim. He's a Physical God who is capable of eating the souls of the dead in Sovengarde and the only thing that can stop him is an Elder Scroll or The Dragonborn himself. There's a reason he's called "World Eater"; he was born to destroy the world.
The other Dragons are no less strange. The Breath Weapon a dragon uses against you? That isn't some magic or natural flame. That is the dragon shouting the word "fire" at you in their native tongue. Their immortality? It might be due to the fact that they exist outside the effects of time. The very concept of "finite", "mortality" or "entropy" is harmful to them. They might not even be truly dragons, but physical manifestations of aspects of the God of Time, Akatosh. Thus, they may be more like demons or angels than traditional dragons. They also can't be killed by anyone but the Dragonborn, a person born with the soul of a dragon, who can absorb their souls. This, along with his/her ability to use the dragon's language without the lifetime of training most mortals require indicates that the Dragonborn might even qualify as a Humanoid Abomination.
The third Epic Battle Fantasy game's main villain, Akron. Awakening him causes even the area around him to undergo drastic effects: the farther location is implied to become an errupting Lethal Lava Land, while the points closer to him are outright made into a very bizarre space area with a black hole behind him.
In Epic Mickey, The Phantom Blot has been changed to be one of these. He was unwittingly created by Mickey and left to corrupt the world of forgotten toons for decades.
Eternal Darkness: Sanity's Requiem takes one of the most interesting twists, as the most powerful Ancient, Mantorok the Corpse God, is actually mildly fond of humanity, even serving as a fertility god in a small village in Cambodia. He's ultimately responsible for the main character's destruction of the "evil" Ancients, using the Roivas family to kill three of the other Ancients in three separate timelines and then merging those timelines together. Denis Dyack, who founded Silicon Knights, the company behind Eternal Darkness, confirmed in an interview that yellow is definitely the colour of a fifth Ancient, supposedly the equal-but-opposite of Mantorok.
Fable The Journey reveals ones which come from the same source as the Crawler: the removal of the Void/Court induced wasting illness of William Black the human who defeated Jack of Blades and the rest of the Court (the illness came from fighting the Court in the first place).
One of the religions in the Civilization mod Fall from Heaven is called Octopus Overlords. The priests use homeless people as channels of the will of the Overlords. The unfortunates Go Mad from the Revelation, which works just fine for the priests, as they are unable to alter what they "hear". One of the things the Overlords teach their followers is how to turn people into zombie-like creatures by drowning them. Interestingly, one of the heroes given to civilizations that follow this religion is said to be the origin of the Overlords, as he has the uncontrollable ability to make his dreams real.
One of the chief reasons Fatal Frame is so scary is that it avoids this trope: all the ghosts are humanoid and that much more frightening for it. Except one: Utsuro from the Xbox version of Fatal Frame 2. It's fought at the end of Survival Mode, in the Hellish Abyss. It emerges from the * itself and resembles a giant... mass of... stuff with short stumpy arms and a vague face. It's described as a manifestation of all the pain and despair of the people who have died there, and it constantly makes noises that sound creepily like a bunch of people sobbing in terror. Fortunately, the Camera Obscura still works on it.
Fate/hollow ataraxia has Avenger, who's described as being an empty space in reality. The form you see is where "NOTHING" is.
In the FEAR games, Alma gradually becomes one of these as the series progresses. She starts out as simply a whispered presence flitting about at the edge of the Point Man's vision, occasionally emerging to inflict horrific violence on bystanders, up until Harlan Wade releases her from the Vault. At that point, her power is fully unleashed, and she heads into full-on Lovecraftian horror that ressurects bodies, brings spirits of massacred civilians back as violent wraiths, and is surrounded by miasmic otherworldly tentacles and appendages whenever she manifests her physical body. By the third game, Alma's presence is ripping reality apart, causing manifestations of demonic beasts and hostile physical spirits, as well as driving the civilian population of the city to madness, turning them into savage cultists that worship her.
Exdeath in Final Fantasy V. He just plain is the part normally and really looks it in his ultimate Tree from at the final battle and as Neo Exdeath. He was born from an aggregate of evil souls sealed into a sacred tree, and later becomes an embodiment of The Void.
Those nameless... things that lurk below the ocean floor.
Kefka from Final Fantasy VI, once he absorbed the three goddesses, stands atop a large tower of human flesh and organs whose floors represent the levels in Dante's Divine Comedy.
In Final Fantasy IX, Necron fits this to a T, with the effect being accentuated by horrific scenery and music. Necron (like Amarant) was a replacement name chosen because the original would have exceeded their name character limit. Its original name? "The Darkness of Eternity".
In Final Fantasy X, Sin is a giant monster the size of a city that emerges from the depths of the ocean to completely annihilate all settlements larger than small villages at random intervals and terrorized Spira for a thousand years. Even if it is defeated by a High Summoner, by sacrificing himself and his friends, it returns a few years later by reincarnating from the body of the High Summoner's closest friend to continue its rampage. Sin leaves swarms of smaller monsters in its path and everyone who survives coming into contact with its toxins (fortunately) suffers from massive memory loss. And apparently, it can wipe out entire armies by causing distortions of space.
Yu Yevon and The Final Aeon. The former is the still lingering sentiment of a long dead summoner who frequently possesses Aeons for the purpose of destroying the world and is the unholy will powering Sin. The latter, while benevolent (usually), is powerful, and its warped form is crafted from the loving sacrifice of a Guardian for his/her Summoner. An example is Seymour's Anima, whose domain is pain.
Final Fantasy XI brings back Atomos, everyone's favorite inter-dimensional nightmare from V and IX. This time, it is actually quite capable of devouring a timeline.
The world of Ivalice in Final Fantasy XII is so heavily populated with Eldritches, it's a wonder anyone is still scared at this point. All of the summons are varying degrees of this, plus the final boss of the sequel DS game, the Occuria...
The Fal'Cie from Final Fantasy XIII are also this, despite looking for the most part like bizarre machine-things.
In the sequel there's Gogmagog, an abomination that the above mentioned Fal'Cie had to throw out of the time-space continuum to be rid of.
In Final Fantasy Tactics, practically every major enemy in the game transforms into one of these at some point in the game.
Final Fantasy Tactics A2 has the Neukhia, whose presence is so dangerously poweful, even having a LIMB in Ivalice presents an apocalyptic threat
Five Nights at Freddy's: Golden Freddy is implied to be this. He appears inside your office (even if both doors are closed) if you see his face on a poster, like he teleported inside. If this strange creature appears, he'll make you hallucinate for a few seconds before he suddenly appears in your face and kills you. He doesn't cause a standard game over; he just crashes the game.
In one fan-made campaign for Free Space 2, Transcend, the Big Bad is a being known only as "the Transcendant", who distorts the laws of reality itself just by being there and unconsciously evokes human souls to play out particular roles. It turns out that the Transcendant was originally human and was somehow expelled from the physical universe, growing into an Eldritch Abomination, then attempted to return home only to very nearly break the universe in the process. He did none of this on purpose either, being pretty well insane by the time he attempted to re-enter reality. All you hear from him directly is his static-broken voice over your radio begging for help... and thanking you when you finally kill him.
In the FreeSpace 2 mod Blue Planet the Shivans appear to follow this trope, as they are implied to be immortal and eternal, transcending universes, not so much a species as a facet or function of the fabric of reality itself. One sequence has the main character psychically connect with them, which places enormous strain on the mind. The main danger in the mission is to prevent the character from being driven irreversibly insane by what she's seeing.
As of Guild Wars 2 there is the six Elder Dragons. Each of which essentially embodies one of the worlds elements. Water, Earth, Ice (winter in general), Fire (Lava), Death (Undeath), and Crystal. Together these six monstrosities were responsible for the extinction of almost all life on Tyria in the previous age. Only a handful of races survived. Their touch brings corruption of all life that comes into contact with them (with the exception of the Sylvari). While they may not be insanity incarnate, they certainly are chaos incarnate.
Cubia. Okay, sure, it's a computer program, but within the realm of The World it's referred to as "The Anti-Existence", specifically of the Twilight Bracelet/the avatars (which are the same things in different forms). As long as they exist, Cubia will exist as well. All of the other AIs running about seem to have some purpose that they're trying to accomplish, but Cubia pops up out of nowhere, and with a somewhat vague explanation of what it is, no one in the series seems to be able to explain what its goal or purpose is, nor how it was created. Oh, and it's unkillable, save for one very specific method the heroes are understandably reluctant to use.
Morganna is called "Old God" in-universe. Before Aura's birth she was the core of The World itself, and is never actually seen in the games in a form of her own, which gives her that Nothing Is Scarier and Ultimate Evil effect. When she actually does take action, it's through the Phases, which qualify as lesser Abominations themselves.
The GMan of Half-Life is many magnitudes more powerful than anything else in the series, casually freezing or warping time and stepping into scenes as if through the fourth wall, and required the entire Vortigaunt race working together to even stall him (which didn't last long). He at least appears human, but is neck deep in the Uncanny Valley (such as being the only character whose face is perfectly symmetrical) and generally behaves as if he studied human speech and mannerisms without having any idea how they actually work.
The Flood, a Hive Mindedparasitic entity of such ancient, alien power that even the near god-like Forerunners were ultimately forced to sterilize a galaxy to put them down... and they eventually rose up again, with the Gravemind calmly pointing out the second time it is being destroyed that this victory will simply delay the inevitable.
The Gravemind on its own: a vast, immortal, reincarnating intelligence. Its physical form is a vast Flood hive full of tentacles and Flood combat forms. If this body is destroyed, it can rebuild itself if but one Flood Spore survives. It doesn't even have to be from that hive specifically. Any Flood under its control will do. And if that nigh invincibility isn't enough, the Gravemind also has telepathic abilities which it can project across interstellar distances. Factor in its love of trochaic heptameter and morbid metaphors and you have one creepy abomination.
The Prisoner from the Cryptum novel. Described as a huge, misshapen humanoid with four arms and compound eyes on an indescribably ugly face. And to top it all off, its kind created the Flood. The sequel reveals the Prisoner to have lied: it was a Gravemind.
The Forerunner Saga delves even further to reveal the Floods origins, the Flood are in fact the Percursors themselves, who have mutated themselves into the Flood so they can have their revenge on the Forerunners, and all of their creations.Halo: Silentium proves the Precursors themselves to be this full out: incomprehensibly complex beings that can take nearly any form they wish, physical or even incorporeal, from the Hive Mind Flood to the monster imprisoned on Charum Hakkor to even the metaphysical memory-bank called the Domain. Their morals and thought patterns are utterly alien (the Didact put it best: "The concept of will, good or ill, is irrelevant when speaking of such beings"), they're driven by an intrinsic need to create other beings, and they're pissed at their creations for wiping them out.
Would you believe that Hatoful Boyfriend has one? The sequel, Holiday Star, has The King, once an unstable and betrayed button quail named Nanaki Kazuaki, now a monstrous Hive Mind that sprouts multicolored extra heads when angry, kidnaps our heroine and her birdy beaus to his Fisher Kingdom, and tries to absorb any souls he encounters, living or dead, out of desire for friendship without betrayal.
The Serpent Riders from the Heretic and Hexen games are immensely powerful alien demons from beyond the crystal wall at the edge of normal space that slipped in when it was damaged. Only one of them really has the Cosmic Horror look, though - Korax from Hexen, who is a bizarre humanoid-reptile-Xenomorph thing. "Surely even hell would never spawn such a being." (D'Sparil looks like a cowled wizard, admittedly riding a humanoid serpent, and Eidolon like a more regular demon.)
The Virus in Homeworld: Cataclysm. The local Precursors apparently picked it up in subspace and disabled their ship in an attempt to contain it. They failed, obviously, and once it was released it assimilated everything it could find, from people to entire ships, absorbing it all into one colossal galaxy-wide Hive Mind with the aim of assimilating everything.
Following the destruction of Dirge and the desecration of the Water Dragon's body and spirit, the agonized spirits of those who died in battle were trapped in an unending war between worlds. The resulting spiritual wound in the world was so great that the Nameless Evil, a purely malevolent force that feeds on the mental anguish of the dead, growing ever stronger, was able to find its way into the world. The Water Dragon and other gods had no power over it, because it came from outside of the world and it had no role in the grand order that governs mortals and gods alike.
There is mention of Death's Hand outgrowing his form and becoming a monstrosity in the Closed Fist epilogue.
As far as we know, Kerbal Space Program doesn't actually have any of these. However, a certain series of bugs that caused spaceship parts to flail like crazy, accelerate in weird directions without any reason, and even spontaneously implode, without going over what it does to unprotected Kerbals was called the Deep Space Kraken, with any and all spaceships and Kerbals who died to the bugs being devoured by it. The name stuck, and any similar bug that came in after the original was fixed has been blamed on this creature.
Kid Icarus: Uprising has monsters such as Ornes, the Chaos Kin (to a lesser extent), and the Soul-Eating Monster.
The Heartless, while still being cute as a button. Their ultimate goal is to devour the hearts of people and entire worlds and turn them into beings like themselves, and they can never be truly defeated because they come from the darkness in people's hearts. It's later revealed that pureblood Heartless were always around and can exist in harmony with the world. It wasn't until emblem heartless were thrown into the mix as a result of Ansem's experiments that they became a world-eating, heart-stealing menace, and as a result, Nobodies came into being as well.
Their counterparts, the Nobodies. Being the remnants of a powerful being absorbed by the Heartless, they are beings that stand at the exact edge of existence itself. They are essentially human-shaped voids, but, unlike their dark cousins, retain their human memories and intellect to properly use their new power. They're also not all bad, Roxas and Namine being genuinely nice and Axel, while not strictly good all the time, has good in him. It's also, oddly, a temporary ailment, as the void can naturally be filled with a new heart overtime.
Unversed are created from the dark emotions in people as a result of the laws of the world becoming unbalanced by the creation of a being of pure darkness, Vanitas. Just Vanitas being near someone with negative thoughts will spawn an Unversed creature and he can also generate them on his own. They are "Unversed" because they are unversed in the complete ways of the world, being composed only to dark emotions such as anger or jealousy.
Xion is halfway between this and Humanoid Abomination, and also one of the few generally nice examples. While generally humanoid, their appearance changes based on the memories of the observer, having been described as male, female, and puppet-like by different individuals.
Unsurprisingly to anyone who knows KoL penguins, they released it next year at the end of Crimbo 2009. The player community brainwashed it into becoming the new Uncle Crimbo, and it showed up in the 2010 Crimbo event... as a Corrupt Corporate Executive running the bland, soulless corporation CRIMBCO.
The end of the Sea questline has you face one of two elder gods of the Mer-Kin: Shub-Jigguwat, the Elder God of Violence (who resembles a giant suit of animated armor super-charged with electricity), and Yog-Urt, the Elder Goddess of Hate (who resembles a giant floating ball of flesh with a huge mouth whose inside is a void emptier than the vacuum of space).
Dark Matter is an immensely powerful, formless being of evil that corrupts all it touches and is completely invincible, except to special weapons. Further, judging by how often it's reappeared, it appears to be impossible to permanently destroy and can only be temporarily defeated. It's even creepier when considering the setting. Thankfully, it's also far more defeatable than most major abominations.
Kirby's proposed origin in the anime series more or less reveals that he himself is an Eldritch Abomination that went good, which explains a lot (though the anime is in an Alternate Continuity from the games). Gooey, his sidekick from Dreamland 3, is a piece of good Dark Matter, too.
Marx. He spontaneously grows plants made entirely out of spikes, can generate knives from nowhere, and can rip himself in half to create a hole to a dimension made entirely out of pain.
DarthNihilus, who Was Once a Man but, through sheer hatred and hunger, became effectively a vampire feeding off of Force energy, wiping out (nearly) all life on at least one planet by his sheer presence, and it is implied that he would eventually grow in power to the point where he could kill everything.
The Jedi Council consider The Exile to be one of these. The real reason she was exiled in the first place was because they were terrified of her nature as a Force black hole. Ultimately, it's this peculiarity that allows the Exile to defeat Nihilus.
In La-Mulana, despite all the big, ugly bosses, the real award goes to The Mother, who is actually the entire temple itself. It helps with the non-euclidean geometries of the temple, and the different areas have no correlation in how they are connected. Oh, and the fact that the Mother came from the sky and created life (e.g. us) in the hopes that it would find a way to return her there.
Cho'Gath, Kog'Maw, Kha'Zix, and Vel'koz are all extradimensional horrors from the Void, which is crawling with them, while Kassadin and Malzahar are humans who take power from it. One was irreparably changed by it and managed to keep his free will (and now fights against it), while the other became a willing slave to it.
Fiddlesticks is an extraplanar being of pure fear who emerged as the result of a botched summoning ritual and was trapped inside a scarecrow.
Xerath was a mage who performed an extremely dangerous ritual that transformed him into a monstrously powerful Energy Being of completely inhuman morality.
Nocturne is a dream elemental of some sort who murdered Summoners in the dreamworld until he was dragged into the land of the awake.
Lissandra was a human who sold herself to primal ice spirits and turned into a horrific elemental who, with their help, nearly brought about the end of the world centuries ago.
Bacterion, Dr. Venom, Gofer, and Zelos, from Gradius are all Eldritch Abominations with the ability of regeneration and cell division. Dr. Venom wasn't always like this though.
The Elder God of Legacy of Kain fame claims to be an omnipotent demigod, existing beyond any casual interpretations of time and space as "The Engine Of Life" that turns "The Wheel Of Fate" and physically manifests himself as an enormous mass of eyeballs and tentacles. It is eventually speculated by the protagonists that he is little more than a parasite who feeds on the souls of the dead, masquerading as an omnipotent god to strike fear into the hearts of his servants.
Big BadsMajora, DethI, and Bellum seem to have some level of this. Particularly Majora, as it is completely unknown how the mask came to be. According to the manga, the mask is the remains of an old god (this works well with the fact that after each boss battle you get "[Boss]'s remains" which takes the form of their mask). This mask then started to Mind Rape the sad lonely imp who started using it until he was its puppet to destroy the world. Majora's Mask made Skull Kid poison the water, create a never-ending winter, poison the ocean, and raise the dead. In the final confrontation, Majora abandons Skull Kid and posesses the Moon, at which point the Four Giants, the ancient protectors of Termina, can no longer withstand the power of the moon and begin to collapse underneath it. Then there's the boss battle itself, which can only be described as a psychedelic brawl.
The Imprisoned and its true form, Demise, in Skyward Sword. However, Fi's analysis indicates that Demise takes a different form every generation... meaning even after it transforms, the form Link faces might not even be what it truly looks like.
Midna takes a bizarre and all immensely powerful form when using the fused shadow. The helmet turns her into a multi-armed trident wielding creature, somewhat larger than Ganon. The impression given when speaking to the spirit Lanayru is that the fused shadow is capable of breaking reality and the last time it was used he and the other spirits had to intervene and break it to prevent it's users in controlling the Triforce through its power.
The Destroyer from The Legend of Spyro: Dawn Of The Dragon counts. It's an ancient mythological monster who's existed since the beginning of time. It exists for only one reason: to cause the end of the world in a wave of fire and ash when unleashed. Oh, and it's as big as a mountain and made of rock and lava. The only way to actually stop it is to destroy every Dark Crystal in it's entire body, including flying inside it and blowing up its heart. That didn't stop it because Malefor, Chess Master that he is, had a backup crystal ready just in case.
Leave it to the designers of LittleBigPlanet 2 to make an Eldritch Abomination out of a vaccum cleaner! The Negativitron travels the cosmos, constantly sucking up all material in Craftworld. It can also be considered an Eldritch Location, too.
Zophar, from Lunar: Eternal Blue. A colossal, floating monolith, whose body is a black tower extending from the heavens, leading down into a face resembling an Olmec Indian sculpture with glowing red eyes and skeletal dragons for arms. He feeds off the hatred and evil in the hearts of humanity, feeds these emotions in order to gain strength from it, and, when he's grown powerful enough, physically manifests in the form described above. His goal? To gain the power of creation from the goddess Althena and remake the entire universe as he sees fit. And if his fortress is any indicator, it's going to be very icky. He's substantially less scary-lookingwhen he does get the power of Althena. His aims are still plenty terrifying, though.
The Soulless Ones of Lusternia. Prototypes of the eventual template used to create the Elder Gods, they were born without souls and exist solely to devour - Gods, infant Gods, mortals, nature spirits, animals, and each other. They imbibe the power of those they devour, making them stronger with every meal. By the present day, only five remain, but those five have devoured so much of reality that they can no longer be destroyed, unless you want to take down the universe with them, so they're sealed away. For the time being...
The strongest, worst thing in the world. A concentrated mass of power, this being hints that the end of the world is near...
The W'rkncacnter from Marathon Infinity. It is described as a being of pure chaotic energy that can warp reality and was sealed inside a star until released by the Pfhor by accident. It is believed that the alternate timelines the player character jumps to are due to the W'rkncacnter's influence.
Invoked by The Reapers, a bunch of Sapient Ships who use gravity and mind manipulation technology to pass themselves off as incomprehensible gods from beyond dark space. They make a pretty good show of it, with Indoctrination working exactly like you'd expect someone having their mind corrupted by terrible beings from Beyond to work (with an Apocalyptic Log in Mass Effect 2 of someone falling victim to it reading like it came straight from the pen of Lovecraft himself), and they certainly have the attitude of something eldritch and unstoppable.
Sovereign:You touch my mind, fumbling in ignorance, incapable of understanding... you cannot even begin to comprehend the nature of our existence.
Leviathan from the Leviathan DLC, The Remnant of the species that created of the Reapers, and used similar manipulation to make all life in the Galaxy worship them as gods.
Metroid Prime has the sentient planet Phaaze, composed entirely of The Corruption which produces more abominations known as Leviathans, and hurls them into space to spread phazon to other worlds. The Leviathans are powerful enough to rip space and use wormholes to travel to other worlds, and under the guidance of Dark Samus, phazon was nearly spread throughout the entire galaxy. It's implied that the planet seen is only a part of it, the rest extending into other dimensions.
Phazon itself is somehow all interconnected, regardless of distance and Phaaze being in an alternate dimension. It appears to be a highly toxic and inanimate fuel source to conventional beings, but it clearly exhibits a will of its own in the large scale and can sometimes be heard laughing at Samus when she passes by pools of it.
Phantoon. It's a ghostly... thing that inhabits abandoned ships. Its primary projectiles are eyeballs made of blue fire and it can turn invisible and intangible and open dark rifts and summon flying disembodied hands with eyes in their palms. It itself resembles a sea creature of some sort (with Combat Tentacles, naturally) with a gaping toothy maw... which houses an eye. And no apparent throat. This creature just makes no sense. Metroid: Other M concept art shows that Phantoon has a humanoid-shaped body to go along with that tentacled head and disembodied hands. The reason the head and hands are disembodied, though, is because he pulls the common Eldritch Abomination trick of having most of his body existing in dimensions the human senses aren't built to handle.
The eponymous Metroids are an entire species of energy-sucking monsters that have repeatedly threatened to annihilate galactic civilization. The jellyfish form commonly encountered are the infants, while the adult forms resemble gigantic alien reptiles or insects, culminating in asexually-reproducing queens. And that's just the natural variety; through artificial modification, they can become all but invincible by removing their weakness to cold, or mutated via exposure to phazon. Attempts to understand their ability to siphon Life Energy almost universally end in failure and/or death for those making the attempts.
Although the entire Ing species could count, special mention goes to the Emperor Ing, the largest and most powerful of them. The swarms under its command nearly annihilated the Luminoth, feeds on the Light of Aether, and can even expose itself to phazon without harm.
Gorea single-handedly annihilated a species of Benevolent Precursors, the Alimbics, going from a formless mass to a bastardization of their form. Even after being contained, it was powerful enough to broadcast Schmuck Bait across the galaxy to lure the hunters to its prison and release it. The thing is practically invincible, easily overpowering the other hunters and proving immune to almost any weapon.
Vorgis in Mugen Souls is enormous, roughly planet-sized and looks like a mix and match of various beasts thrown together with neon veins popping out. His entire existence is based around eating planets whole. He was once a very disobedient pet of a God of Destruction.
The Mask of the Betrayer expansion pack for Neverwinter Nights 2 lets you create one by stuffing a legion of evil and insane murdered souls into the withered husk of a dead bear god. And then the absolute "Evil-With-A-Capital-E" ending has you become a soul-devouring abomination capable of unmaking gods.
In the new chapter in Persona 3: FES, the team discovers Erebus (Nyx's husband and brother in Greek myth). Aigis and company learn that their grief over the hero's death not only manifested the Abyss of Time, but also helped fuel Erebus, the Anthropomorphic Personification of nihilism and sorrow in human hearts. This "nihilism avatar" was the real problem, not Nyx — Nyx existed long before humanity ever awoke and, by itself, wasn't a force of good or evil — it was only when the self-destructive thoughts in Humanity hit a critical threshold that they coalesced into the decidedly unfriendly Erebus, who seeks to absorb Nyx's power and bring about The End of the World as We Know It. The hero wasn't sealing Nyx away, but instead keeping Erebus away from Nyx. The party fights Erebus in a final battle and learns that the protagonist can never return to them, because so long as there is the desire for destruction in human hearts, Erebus will live on. However, a stated goal of the presumably immortal Robot Girl Aigis is to work to improve humanity to the point that Erebus can be defeated — someday.
The Waterwraith boss from Pikmin 2. Its mentioned as being anchored in another dimension and capable of causing fear to the point of insanity.
Pikmin 3 has The Plasm Wraith, the game's final boss a sentient moving blob of golden goo with a strange cube in the center, that appears vaguely humanoid at times. It's based off the Umibozu of Japanese folklore, an equally eldritch monster that destroys ships and keeps the treasures and captains for itself, a fate Olimar nearly suffers. You can't even kill it, as when you leave the planet in the ending, it's fully reformed at full power, roaring in anger as you blast off.
Missingno. and its glitchy ilk fracture reality by their very presence (music, graphics, and save data are twisted), possess bizarre dimensions ('M is 23 feet tall, and Missingno. itself is more than three thousand pounds), and if exposed long enough, the protagonist's mind shatters entirely (the game crashes). As essentially junk data given form, to the player character they might as well be Primordial Chaos.
The glitch Pokemon whose name is only represented as a female symbol gets a special mention. It has an endless cry that actually sounds like a bizarre twisted song, it's base stats are second only to Arceus, it looks like Giygas, and finally, it weighs 3 tons and is 80 feet tall.
Arceus itself, who despite being widely thought as the Pokemon equivalent of God (who has His own extensive entry) is actually closer to Azathoth, considering it created the universe largely by accident then went to sleep for a few billion years.
Dialga and Palkia, Arceus first creations, are Space and Time personified (indeed Time started flowing with Dialga's creation) and their dominion over them is absolute. Their battle in the tenth film had so much power being thrown around that each of their attacks were damaging reality.
And then there are the Unown. While they're a Joke Character individually, they're a powerful reality-warping Hive Mind in groups of hundreds. They come from their own dimension, live in inexplicable ancient ruins, and make incredibly creepy radio transmissions to boot. Oh, and Arceus uses them to make a new Dialga, Palkia, or Giratina in HeartGold/Soulsilver.
In the Jirachi Wish Maker movie, the villain Butler attempts to create a Groudon using Jirachi's wish granting powers. The result is a bizarre demon that looks like Groudon, but it's pretty easy to tell it's not.
To a lesser extent, Groudon, Kyogre, and Rayquaza. Ancient, slumbering entities responsible for the enviroment, they're millions of years old and, when awoken (well, not Rayquaza), start to cause the end of the world. Expies of the Behemoth, Leviathan, and Ziz, who are cosmic horrors on their own, they may very well be Pokemon Great Old Ones to the Creation Trio's Outer Gods.
Pokémon Mystery Dungeon: Gates to Infinity has the Bittercold, a non-sentient crystalline entity that embodies the negative feelings of all the Pokemon in the world and feeds upon said feelings to strengthen itself (which is a bit of a problem considering the game's setting). Pokemon suffocate simply from being near it and it ends up growing powerful enough to threaten the world's very existence.
In Prototype2, the Blacklight Virus now has a new host: James Heller. And his powers are far more monstrous than Alex Mercer's in the first Prototype, thanks to his "tendrils" power. Whenever tendrils are involved, the result is masses of flesh dangling from the buildings with strung-up corpses caught like flies in spider silk.
The entire setting of Prey, albeit being techno-organic alien in nature. Big enough to host every level save for the introduction and ending and never seen in its entirety. Reality-violatingly ugly as in portals, spatial anomalies, and multi-directional gravity. Happens upon the Earth on one night without any warning. It is implied that it seeded Earth with life just so it could come back and eat everyone. And they can, apparently, invade the spirit realm via portals, although even they are taken aback by the sudden spirit activity.
Quake has Shrak, the final boss of the expansion pack.
In Resident Evil the Las Plagas itself may be this. It was found a hundred years prior to the story, centuries before Umbrella employed its scientific techniques to produce its famous viruses. Its also worth considering that the Plaga were fossilized when they were discovered. So while they were discovered hundreds of years ago, they could be thousands, millions or billions of years old.
In Return To Krondor, the Dark God seems to be this. An entity that is very dangerous and had to be sealed away. A group of depraved individuals worship this god and want to release it into the land of Midkemia. Releasing it would be a Very Bad Thing To Do.
While the six dragons in Rift are explicitly stated to be mere manifestations of the Elemental Lords, Akylios takes the cake; his description mentions he was mad BEFORE he started gathering all knowledge and that he doesn't actually care what all the other dragons do...
The Inadequacy and other monsters fought during "Dream Mentor", all of which are embodiments of Cyrisus' negative emotions.
The Spirit Beast is a monstrous ghostly thing that lives in a parallel spirit dimension where it feeds off the souls of ghosts who became trapped there (inflicting And I Must Scream on them). It was trying to break between dimensions into the world of the living so it would have more souls to feed off of. The player is completely unable to directly attack it. It is defeated only by the player weakening it through indirect methods and then empowering the ghosts it was feeding off to be strong enough to finish it. Unfortunately, because of the properties of the parallel spirit world it was killed in, it death resulted in the manifestation of a Corporeal Beast in the real world. Luckily, the Corporeal Beast can be harmed by normal attacks, so this is better than if the Spirit Beast had escaped, but it still is one of the most dangerous monsters in the whole game.
Muspahs are bizarre monsters manifested from the dreams of a comatose and unintelligent elder god. They are what the Mahjarrat, a race of Humanoid Abominations created by the same elder god, have nightmares about. Said elder god, known as Mother Mah also created Seren (ironically, one of the nicest of the gods) and Zaros (the most alien of the gods, who when on to create abominations of his own, known as the Nihils.). The world she rules over is a Death World.
The inhabitants of the Abyss and the Infernal planes. The ones that players most commonly encounter look like typical demons but the rest are far more alien. The Abyss itself (which is the dimension that allows teleporting to work) may be one, because it looks like the insides of some huge fleshy monster full of teratomas. It has been implied that the part of the abyss we have so far seen is inside the remains of the gigantic Chthonian demon Hostilus; Chthonian demons have the ability to assimilate the essence of whatever they eat and grow bigger and more powerful.
The Big Bad of SaGa 3 is a blobby mass of goo and tentacles which can absorb the power of a Physical God via Body Horror. Plus creating an Eldritch Location outside of time and space. As the most powerful of the setting's divine creatures, it could easily be a stand-in for Azathoth.
In Sam & Max: The Devil's Playhouse, Yog-Sototh, who looks suspiciously like Cthulhu and has many of the attributes of a cosmic horror, makes several appearences throughout the season. In episode 304, he is actually seen. Then there's Junior, who is even more fearsome, and Maxthulhu, when Max's psychic powers combine with Junior's Taint.
Sanity: Aiken's Artifact has individuals given psychic abilities. The psychic abilities, however, cause individuals to become insane if they are overused, and these abilities were given through an artifact that was planted by a Sanity Devourer, who will harvest a planet once psychic abilities become commonplace enough for easy eating.
Septerra Core. Ouroboros is a giant monster that dwells somewhere near the Core of the world and is said to be as old as Septerra itself. It can be summoned with Fate Cards to inflict massive fire damage to the target and the only part of it seen are its three heads. That alone is comparable in size with other, rather huge summons. And it isn't known how large the rest of its body is. It's also rumored that it's an inteligent being and that if its heads ever all agree on something, it will cause The End Of The World As We Knowit.
Shadow Hearts is filled with these things. The Final Boss of the first game, Meta-God, is a Sufficiently Advanced Alien crossbred with a horse and is beyond human reasoning.Covenant sets up Amon, one of Yuri's strongest Fusions from the first game (second to Seraphic Radiance), as part of a triumvirate of eldritch horrors, opposed and matched by Asmodeus and Astaroth.
Shadow of the Colossus features Dormin, which refers to itself in the plural, is able to resurrect the dead, was sealed inside the bodies of 16 giants (the colossi) and gradually begins to take over the body of Wander, giving him black veins and a pale almost dead complexion. When it takes over him entirely at the end to prevent Emon from killing Wander it turns him into a colossus wreathed in shadow and so massive that he can't move inside of the cathedral, even when practically lying down, allowing Emon to kill him with ease, but even without a host and seemingly nothing attaching it to the world anymore Dormin is still able to bring Wander back as a baby (albeit one with horns). Also the colossi are implied to have been made to seal it away are were made very damn hard to kill for the reason to keep it out of this universe.
Not only is Shikkoku No Sharnoth full of these in the form of the <<Metacreatures>>, but M, the protagonist's cryptic guide, benefactor, and possible love interest, is later revealed to be Nyarlathotep.
The eponymous Genius Loci of Silent Hill feeds off of people's emotions, magnifying and returning them. Originally it was a place of healing and safety, but centuries of death and suffering turned it savage, inflicting pain of it's own in a positive feedback loop. Then the local Religion of Evil had the bright idea of focusing all that misery into one little girl in the hopes of birthing a "God" to turn the world into "paradise". Long story short, the town became outright malevolent, trapping people in a nightmare of their own creation to feed and become ever stronger, eventually spreading far beyond the borders of Silent Hill itself.
Sin and Punishment: The inhabitants of Outer Space (which is apparently a separate dimension/realm/something from the space we know, which is called Inner Space) are described like this. They are not alive in any sense known to Inner Spacers, and can shapeshift to mimic anything... including entire planets. They are defeatable, but it is really not easy to do (and the only inhabitant of Outer Space we see seemingly effortlessly survives the heroes' efforts to eradicate it, though they are unaware of this). Even some of the Inner Space characters get distinctly Lovecraftian at times; see Armon Ritter of Sin and Punishment: Star Successor, particularly his final form.
Much of the horror that occurs in the first Siren is the result of a village of people eating one alive out of desperation.
Skullgirls has the Skullgirl itself, the result of an evil artifact known as the Skull Heart transforming women who use it to make ill-considered wishes. Marie, the current one, looks like an ordinary girl until she's greatly threatened - at which point she turns into a hideous creature made of assorted bones.
Chaos, from the Sonic Adventure. However, it is usually benevolent, but was driven to evil by Pachacamac's Moral Event Horizon. It turns good again at the end of the game.
There's also the trio from Sonic the Hedgehog (2006): Iblis, a massive beast of destruction made only out of fire; Mephiles, a gasseous-liquid mind of complete corruption and shadowy powers; and Solaris, an interdimensional being trying to destroy reality.
In Sonic Generations, there's the Time Eater. While most of its presence in the game is as a robotosized/cybernetic vehicle operated by Robotnik and Eggman, Eggman reveals its natural purpose, when he discovered it, is to erase time, making most of what the Eggmen have it do already a natural ability. Between that, its looks, and the dimension the game takes place in, as well as the location of the last boss fight...
Spectrobes practically runs on this trope. The main villians are the Krawl, which are amoeba-like monsters that are bent on destroying planets, the smaller ones are simply living blobs, while the larger ones are more eldritch the bigger and more powerful they are. The High Krawl, ESPECIALLY Jado, who refers to himself as "The Great Negative". Krux, the Big Bad of the series, is a Humanoid Abomination.
The "Corrupted" in Splatterhouse are described as arising from the difference between what people mean when they say something, and what other people understand it as meaning—specifically, they're embodiments of the pain and suffering that often results from such misinterpretations. As ephemeral beings, they can't exist in this world without a host body, which is for the better, since even an enhanced human can't so much as look at them. (They're willing to make deals with humans, but it's indicated they have no intention of honoring them—maybe not even a concept of honor.)
The Androsynth disappeared before the beginning of Star Control II, and their region of space is now occupied by the Orz. Trying to put together an accurate assessment of what happened on their homeworld results in the scientist who read about the Androsynth's IDF research going insane and being attacked by invisible creatures. If you ask the Orz about the Androsynth, they attack and take no prisoners. It's not exactly clear what went down, but the Arilou put it best: "You do not wish to be seen. The Androsynth were seen. There are no more Androsynth anymore. Only Orz." This is an especially subtle example, because, early on, the Orz seem comical, with their round, bird-beaked bodies, their nearly-untranslatable speech, and their silly voices. According to developers, Orz, as the captain sees them, are actually a *fingers* projection of some higher-dimensional being.
At one point, you can find them above what used to be the Taalo homeworld. For context, the Taalo were exterminated several thousand years ago. The Orz claim to be currently interacting with the dead Taalo, *chasing* them and describing it as excellent fun. They also imply that this will be humanity's eventual fate if they continue to be good *campers*.
In Quasi-Space, part of the background music is quite obviously somethingscreaming. It doesn't ever actually appear, which somehow just makes it worse.
Star Control 3 has the Eternal Ones; they're invincible and feed on "sentience", so they wait for advanced civilizations to develop and then come and harvest them.
The Zerg Overmind. While it's made from normal cellular matter, its "form" is nothing more than a vessel for the collective intellect of trillions of Zerg, with enough psychic power to rip open space-time with ease and bend anyone to its will. It doesn't help that its purpose is to assimilate or exterminate everything, everywhere.
StarCraft IImakes it into a Papa Wolf by revealing that soon after its creation, a... Dark Voice corrupted it and imposed its millenia-old directive of exterminating the Xel'Naga and the Protoss (and presumably everything else). Since the Overmind was created without free will, it could only follow this directive while raging inside its own mind. Not that it ever cared for the Protoss or Terrans, mind you, it just didn't want its own children, the Zerg, to become Cannon Fodder and nurishing food for the Dark Voice and his underlings in their galactic conquest. Hence it created a successor, and set its course straight for Auir, knowing it would likely be slain there - Leaving control of the Zerg in his replacement, who would hopefully not be influenced by the directive. Seems like even Eldritch Abominations has loved ones that they're willing to sacrifice themselves for.
Mario & Luigi: Bowser's Inside Story: The Dark Star's introduction sounds straight out of Lovecraft, and by the time it's inevitably unleashed, it's a sinister blob of darkness that has the Mario Bros choking from simply standing near it. On the other hand, it's up against Bowser, who looks forward to the challenge.
Einst, the inter-dimensional race that claims to have watched humanity from the beginning. Now they wish to "reset" humanity by choosing a new Adam and Eve. They also appear in Hagane no Messiah and claim to be the ones who created the world by creating the Crossgate dimensional portal and turning the world into several mini-dimensions separated by a dimensional wall. It turns out that Einst's goal is to return to the original world, "the world of silence". Their hive mind doesn't recognize individual will and express genuine confusion when humanity foil their plan.
Super Robot Wars D has Perfectio, king of the Ruina, Energy Beings from another dimension. Since Perfectio feeds on despair, the Ruina try to turn Earth into his cattle farm by sealing Earth in another dimension. While it's possible to destroy the Ruina, Perfectio is immortal and can only be stopped by sealing the gate to its home dimension.
Super Robot Wars Z mentions Taichi as the entity that controls the fate of all universes by manipulating the Origin Law. It is also the one that created twelve Spheres that grant their holder immense power and limited access to the Origin Law. However, the holder will slowly lose his or her humanity in exchange for said power. (A small note is that Taichi is from Taoism with some Mind Screw-level properties.)
The Suul'ka of Sword of the Stars are Liir who've grown so old and so large that they cannot survive in gravity wells. Their psi abilities allow them to coerce fleets to join them, feed on the Life Force of entire planets, and they can "teach" their vast and ancient knowledge to their followers. But their minds are so vast and complex that many Zuul who are taught by telepathic contact die, until eventually one feebly mumbles "Eureka... please, Lord, stop..." From the Liir perspective, they're closer to Humanoid Abominations.
Tales of Vesperia has the Adephagos, which is a Sealed Evil in a Can abomination and is released about 2/3rds into the game. It's destroyed by stopping using aer as an energy source and switching to using mana instead. A cookie to those who get the aesop.
Terraria has the Wall of Flesh: an enormous wall of flesh with eyes and mouths that can only be encountered by throwing a voodoo doll of your guide into the lava pits of the underworld, which will chase you through hell until either you or it dies. You can't escape without killing it, but killing him supercharges The Corruption throughout the world, causing it to spread aggressively past nearly all barriers... and introduces a second, opposing style of corruption which spreads equally quickly. And it makes more deadly enemies appear everywhere.
The Last Door heavily features a yet-to-be-explained god-thing referred to as the Bird/King of Birds. The protagonist Jeremiah, two friends, and a priest at their boarding school attempted to look beyond the veil of human perception through some sort of ritual or incantation. Though the game is very vague (as of now, anyway) on what exactly happened, it's clear that they somehow contacted the Bird and it drove them all insane in different ways. As Jeremiah explores the spooky settings of 1890s Scotland and England, the Bird appears in nightmares, windows, and keyholes as a giant orange/yellow eye that screeches and then disappears.
Touhou gives us the Saigyou Ayakashi, a demonic entity taking the form of a cherry tree. It drew people to its side with its beauty, tempting them to sleep under its branches... at which point it devoured their souls. Out of all of the characters in the series, it's one of the miniscule handful that can actually be called evil. Currently it's Sealed Evil in a Can, the body of a powerful young woman being buried beneath its roots to render it comatose; Perfect Cherry Blossom revolves around keeping Yuyuko from unknowingly breaking that seal by bringing the woman back to life (thanks to Ghost Amnesia, she's forgotten that she is that seal).
The Myrmecols from the UFO series are a pretty-much-textbook example: they're enormous, spacefaring creatures with the power to control the populations of entire planets on a regular basis as part of their reproductive cycle.
Warcraft 3 introduced a faction of vaguely Lovecraftian entities, the Faceless, presided over by a stock Eldritch Abomination called the Forgotten One. They were pretty easy to kill, though.
Warcraft also features the Old Gods (of which the Faceless are servants), which are Shout Outs to Lovecraftian entities. They are behind some of the truly nastier fellows who originated in Azeroth, such as corrupting Neltharion into Deathwing along with his entire dragonflight, corrupting Queen Azshara, the most powerful Night Elf sorceress, and creating the Naga, the silithid, the qiraji, and the nerubians. They're also the (partial) creators of Humans, some Giants, Dwarves, Gnomes, and Troggs by using their parasitic weapon, the Curse of Flesh, designed to make its targets more like them and less like the original seed races.
One Old God, C'thun, has, however, been killed by mortals (he was a raid boss). However, he had gotten his ass kicked by the godlike Titans so badly that they thought he was dead, so the players faced him at only a fraction of his full power. Apparently, the remaining Old Gods pulled the fun trick of tying their existence to Azeroth, meaning that if they die, they take Azeroth down with them. There is also the question of whether they can even be truly killed. They are said to exist "outside the cycle" of life and death. Though C'thun is technically dead, it was still able to mutate and transform Cho'Gall into a monstrosity.
The Faceless return in World of Warcraft: Wrath of the Lich King in the form of three Forgotten Ones and Herald Volazj, who are very Lovecraftian in appearance. The Herald periodically causes the player characters to go insane and fight one another. The power behind the Faceless, and all sorts of other weirdness in Northrend, seems to be an Old God named Yogg-Saron (not to be confused with Yog-Sothoth). Just Yogg-Saron's existence beneath the lands drove creatures to madness and its very blood is forged into equipment for arming the armies of undead in Northrend.
Yogg-Saron was featured in a content patch. True to trope, he is able to drive characters insane and make the entire raid hallucinate about past events. Despite this, within twenty four hours, he'd met the fate of all raid bosses. However, it is worth noting that players initially face Yogg-Saron with the help of four previously corrupted guardians that must be slain. The battle without their aid is considered to be one of the hardest in game and was even outright dismissed as 'mathematically impossible' on initial inspection.
With the final major content release, N'Zoth hasn't appeared in person, but it has been revealed that the corruption of Deathwing was so extensive that after tearing off his elementium plates, he transforms into something very like an Old God, complete with a spell that can destroy the entire world. That spell doesn't just kill the raid. It turns the screen completely black, even the chat-box. The only thing visible is the release soul button.
Mists of Pandaria has the Sha, seven black creatures that embody doubt, hatred, fear, violence, anger, despair, and pride. It is implied that they are the remains of a dead Old God, the seven-headed Y'shaarj who was killed by the Titans long ago.
Ragu O Ragula, a monster of practically unimaginable destructive power, appears in every Wild ARMs game. Almost always a Super Boss sealed safely out of human reach (and out of its reach of humanity). Unseal it at your own terror. Well, might be scarier if it weren't a constantly recurring theme in the series.
In Wild ARMs 2, the Planet Eater "Encroaching Parallel Universe" Kuiper Belt does this trope in a decisively terrifying way, complete with music that perfectly captures "too terrible to exist in my universe".
In Xenogears, a being named Deus strongly exemplifies this, even looking irreconcilably bizarre to boot. (Incidentally, Deus is located aboard an interstellar spaceship named Eldridge.)
By comparison, in Xenosaga, it is believed that God Is Evil and one of these... but then it turns out that God is actually benevolent. It's just that His actual form drives them mad.
Galvaran, Jabir, Napishtim, etc. in the Ys series. Many of these monsters were created when the humans who stole the Black Key attempted to recreate White and Black Emelas, but after failing that, infused the resulting Ash Emelas into soldiers.