Alan Wakeimplies that the Dark Presence is one of these; trapped under Cauldron Lake and waiting for someone to set it free...
In Amnesia: The Dark Descent, you are being followed by "things" or "shadows" as you explore the castle. You have no weapons or 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 status). 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.
The Orb Guardians deserve a special mention. They are various unearthly versions of more normal beings, but what they have in common is that non-Chaotic gods seem to be afraid of them. Trying to sacrifice one will result in the god screaming "TAKE IT AWAY!" (A Chaotic god will just tell you they are more useful servants than you.)
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.
The Angels of Paradiso themselves count, especially 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. Breaking off any angel's golden armor and marble face reveals their true alien countenance.
The Demons of Inferno also count, being just as nightmarish and incomprehensible as you'd expect a demon to be. And no, Light Is Not Good does not automatically translate into Dark Is Not Evil; unlike the angels, the demons don't make any secret of being the eldritch monsters they are.
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 abomination.
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.
The Destroyer in Borderlands. It's said to be an entity from another dimension that destroyed the Precursors, with the last one sealing it in a Vault. Of course, the character who said this turned out to be an Unreliable Expositor, but there is some evidence that it's more than just a disused Precursor weapon.
Broken Age: Mog Chothra, a colossal creature resembling a floating brain, with countless Combat Tentacles on the underside, and glowing red hexagons all over its body that might be eyes, but no one is completely sure. And to think that his species is implied have a thriving population. Ultimately subverted, he's actually a robot.
This series' depiction of Dracula is actually closer to this, with a dash of The Antichrist, than to a traditional vampire.
In "Aria of Sorrow," the boss of the Underground Cemetery is this.
Lords of Shadow 2 continues the trend of those by giving us Inner Dracula, also known as the blob of blood and the source of Dracula's powers.
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.
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.
There are also In-Universe theories about another Entity acting on the world, though what it is isn't really clear - most likely, it's the will of the Planet itself. The Entity interacts with the world only through the creation of the Gates that allow time travel, which are described as being like the memories of a dying man; the only time that it unambiguously takes action in the game is when it creates a temporary Gate to allow Lucca to reverse her mother's maiming.
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 Bosses, Exgal and Aekros. Their names cannot be displayed except as bizarre characters, and they have triple life bars that regenerate instantly. Instead, Boki has to destroy their three Ulsev puppets. Each time she does so, she can absorb one of their similarly unnameable but extremely powerful abilities. The skull-like, demonic Exgal only goes down when Boki combines all three of its Black Magic 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. Aekros on the other hand is angelic-looking and is powered by light magic, but is otherwise just as incomprehensible as Exgal, as well as being even more powerful.
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 Bed of Chaos is a tree-like monstrosity that came about from a failed experiment to preserve the dying world's beacon of light, the First Flame. Instead of creating a new fire, the Witch of Izalith spawned what would eventually consume her and some of her daughters, as well as spawn every single demon in existence.
Manus, the Father of the Abyss. The true embodiment of the darkness that dwells within all descendants of the Furtive Pygmy, he's an insane, ape-like creature who wields the power of the world-destroying Abyss and corrupts everything around him, firmly establishing himself as the Squid in Dark Souls's Angels, Devils and Squid scenario. The fact that he was originally human hints at the terrifying idea that all humans have the potential to transform into mindless, superpowerful abominations like Manus if they cannot control the shard of the Dark Soul they inherited from the Furtive Pygmy.
Dark Souls II adds the Rotten, a grotesque amalgamation of writhing bodies that is said to have acquired a Wondrous Soul on its own, something that is said to be impossible. It conveniently resides in the deepest reaches of Drangleic, with nothing to care for except the rejects that fell down all the way to the Gutter.
The Second game also contains the Darklurker, a bizarre, angelic being that exists at the deepest point of the Dark Chasm of Old (aka the Abyss). Said Chasm is an Eldritch Location that can only be reached through dark portals, and nothing whatsoever is explained about the Darklurker, with even its soul description saying "Some things are better off left unilluminated".
Dark Souls III adds Aldrich, who is originally called "The Saint of the Deep", but later another name for him is revealed: "The Devourer of Gods". That title isn't just for show; when you find him, he's in the midst of consuming Gwyndolin, the Dark Sun of Anor Londo, and he wields abilities previously only used by gods in the series (such as Nito's Gravelord Sword, Priscilla's Lifehunt Scythe, and Gwyndolin's magic arrow spam). Aldrich himself used to be human, but after eating many people he "softened and bloated" into a large, mobile pile of black sludge. Despite this, his power is enormous, as he absorbs the power of those he consumes.
Darkest Dungeon has eldritch horrors erupting across an ancestral family's estate, complete with a hideous cosmic abomination that may or may not be the very progenitor of humanity itself, deep beneath the earth. The game's setting is partly inspired by Lovecraft's works.
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 by Daylight has the Entity, which the killers sacrifice the survivors to for an unknown purpose. In game, the Entity is never seen in full, though it has spider-like limbs to snatch up hooked corpses.
Deadly Rooms of Death has the Pit Thing. He manifests as a voice rising from various pits throughout the world and the portrait that appears when he speaks looks like some tentacles trying to squeeze through a crack. When the truth vessels try to describe him, they don't get any further than "a network of gentle strangulations." He refers to another godlike being as his sister, and claims that a thousand of his hearts die every time he makes himself understood. Evidently, he's something that's simply too weird to explain.
Dead Space: At the end of Dead Space 3, the true source and explanation of the Markers and Necromorphs are revealed. The Brethren Moons. They are massive moon-sized flesh beings created from a Convergence Event, where a planet's necromorphs merge together into a giant super-being, the moon. Markers are their form of reproduction. As civilizations suffer from energy crisis, the infinite energy from the Markers lures them in, and eventually creates a necromorph outbreak and then a Convergence Event. Their telepathic powers are beyond anything else in the universe, causing madness and hallucinations on a wide scale and communicating with each other instantly on a cosmic level. The moons are ancient and incomprehensible, but they are smart, and they are hungry.
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.
Dragon Age: Inquisition: The Titans from the Descent DLC are incomprehensibly large beings that dwell deep beneath the surface of Thedas, and are actually the source of all lyrium, since it is in fact their blood. They share a unique psychic bond with all dwarves, indicating some form of latent Hive Mind. They're also clearly sentient, and are privy to unknown secrets about what lies beneath Thedas, and have unexplained powers that allow their thralls to seemingly teleport at will throughout the world. In short, everything about them essentially slaps some well-accepted fact in Thedas in the face.
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.
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.
In Eversion, a major character is one. In the bad ending, she eats you. In the good ending, you're one, too. Not as surprising as you might think, given what he does to the world.
In Evolve, this is the true nature of the monsters. They are the manifestations of a largely unknown force, likened to a 3D being pressing against a 2D universe. Their forms are created by drawing on the subconscious fears of humans, fears that they themselves may have created millennia ago. Killing one merely destroys that manifestation, forcing it back to its dimension of origin until it can remanifest from an egg, which are self-contained interdimensional gates. The monsters themselves can sense dimensional distortions and have limited telepathy, while their genetic code somehow involves the equation used for the reality warping tech of the humans. All of this is meant to perpetuate their end goal: to change the base energy state of the universe to a more stable one, annihilating everything in the process.
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).
Fallen London's world has a whole variety of them, including sentient stars, giant space crabs, cthulhu-looking humanoids, and a nomadic mountain that shouts at you in an eldritch language.
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.
The Fallout series in general seems to have a soft spot for Eldritch Abominations. The Dunwich Company of Fallout 3 and 4 serves as an homage to The Dunwich Horror, a famous Lovecraft story. While no Abominations physically appear, the higher-ups of the Dunwich Company regularly sacrifice humans to their version of the Great Old Ones. Same goes for Lorenzo Cabot in Fallout 4: his son describes an ancient, alien city in the Southwest were his father found an ancient artifact that granted Lorenzo psychic powers and seeming immortality.
The Master from Fallout qualifies as well, given that he's an amorphous blob of flesh fused to a computer and speaks through four voices.
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 II. 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.
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.
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.
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.
There is also the "Great Darkness", which is something which the main character is advised to never ever think about, as even thinking about it puts you in danger of being consumed by it. It is supposedly the thing that the Shivans and Vishnans are attempting to prevent from manifesting. Word of God is that the Great Darkness is not a "being", but rather the ultimate level of cognition and consciousness, simultaneous awareness of everything and nothing... a kind of existential black hole or evolutionary dead end that once an intelligence reaches that point, it lapses into a state of non-being.
Gradius has Bacterion, an alien entity from Another Dimension that endlessly reproduces and spreads its biomass, to the point that it can and has consumed entire planets into its Hive Mind. Worse, killing it permanently would require the complete extermination of all Bacterian cells in the universe: if even one survives, it will eventually regrow into a new Bacterion (might take a few hundred years, though). Bacterion can also transform other creatures into beings like itself, with the same abilities: it has done so to Dr. Venom, Gofer, and Zelos, the last of which was already pretty eldritch on its own. There's also the mysterious creature "Original Visions of Ultimate Monsters" (O.V.U.M.) from Gradius Gaiden, a shapeshifter that may be another piece of Bacterion, or something else altogether.
Grey Goo has The Silence. It's enough of a threat to make an assimilating nanobot go from "explore and map the stars and report back signs of (sentient) life to humans" to "this thing has to be stopped or EVERYONE DIES". This thing has apparently devoured countless stars and is covering a major percentage of the universe. The goo is trying to grow to such proportions to stop it, The Silence devouring everything in its wake. The Beta/Morra claim that everything has a song or story to share, including the goo, originally just an exploration probe. And guess what is the only thing not to have one? It's also making a beeline straight for Earth.◊ All of Silent Space is part of it's mass. It may come from Ecosystem Psi (making it a Pandora's Box) or from outside our galaxy — which brings the question how much of the UNIVERSE has it already devoured?
As of Guild Wars 2 there are the six Elder Dragons. Each of which essentially embodies some of the world's elements. Water (the unknown deep sea dragon), earth and plant life (Mordremoth), ice and winter in general (Jormag), fire and lava (Primordus), death and undeath (Zhaitan), and crystal and lightning (Kralkatorrik). 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, who it turns out are actually creations of Mordremoth the jungle dragon). While they may not be insanity incarnate, they certainly are chaos incarnate. Even worse, it turns out that the dragons are Cosmic Keystones that maintain the balance of magic within the world- and with two of them (Zhaitan and Mordremoth) destroyed, the world is just one more dragon death away from the magic spinning out of control and annihilating everything.
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 are 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 their Gravemind calmly pointing out right after their second defeat 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 accumulated biomass. If this body is destroyed, it can rebuild itself if but one Flood spore survives, anywhere. 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 series delves even further to reveal the Flood's origins: they are in fact the Precursors themselves, who have mutated themselves into the Flood so they can have their revenge on the Forerunners and all of their other creations. Halo: Silentium shows 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. 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, they're pissed at the Forerunners for wiping them out (which they only managed because the Precursors were simply too busy marveling at the violence to defend themselves), and they're implied to be even older than the universe itself. Even their insanely advanced technology is nigh-incomprehensible, being apparently made out of thought.
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.)
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.
Case in point, most members of Organization XIII see Xion as a girl in a hood. Xigbar sees Xion as someone his Other encountered before becoming a Nobody, Ventus. Roxas and Axel both see Xion as an unhooded version of the hooded girl, with a face and voice matching Kairi, only with black hair. Xemnas on the other hand sees his No. i as the form he intended them to be: a perfect copy of Sora.
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).
And let's not even talk about the real final boss of the Sea questline; Dad Sea Monkee hooked up to a reality-bending, perception-warping, quite literally indescribable machine.
The room is the machine occupies the room contains the machine contains the room describes the machine creates the room is the machine.
In Crimbo 2015, the "Earth Mother" the hippy elves are summoning turns out to be Gaia'ajh-dsli Ak'lwej, who's less "benevolent spirit of nature" and more "primordial elemental monstrosity"; it's a hundred feet tall, it has "every kind of eye" on its face, and its body is made of a mish-mash of stone, flesh, and plant matter.
Dark Matter is an immensely powerful, formless Hive Mind that is capable of possessing an entire planet's inhabitants. 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. This is compounded in Kirby: Planet Robobot, where a flawed clone of Dark Matter is created by the supercomputer Star Dream. Not only is it stated that trying to comprehend Dark Matter's form required essentially all of its computing power, it still can only create the swordsman form instead of Dark Matter's true form.
0 (pronounced Zero) itself is the core of Dark Matter and is an entity that looks like a gigantic eyeball. It has complete and utter control over Dark Matter. It later resurrects itself from death as a surreal-looking Fallen Angel called 02 (Zero Two) to fight Kirby again.
The Clockwork Stars are nebulous at best and tend to be incredibly powerful. Their exact strength isn't known, but both Star Dream and Galactic Nova can bend reality itself and cause untold damage to the living mind as seen by Max Haltmann's horrific end in the True Arena ending.
Most Kirby final bosses are at least somewhat eldritch. Nightmare is a wraithlike embodiment of bad dreams whose very death blows up a sizable portion of Pop Star's moon, Dark Mind from The Amazing Mirror is an evil mirror demon, and Dark Nebula from Squeak Squad is a cycloptic black star stated to be the ruler of the underworld.
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 Dream Land 3, is a piece of good Dark Matter, too.
The final boss of Kirby Star Allies, Void Termina, takes the cake. Not only did it take the sacrifices of a cult of extremely powerful mages to summon it, nor that it is stated to be the destroyer of worlds, but it is implied to be the creator of the aformentioned Dark Matter and even Zero. And in case that's not enough, the appearance of its true form heavily implies that it has some sort of connection to Kirby himself.
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, Vel'koz, and Rek'Sai are all extradimensional horrors from the Void, which is crawling with them, while Kassadin and Malzahar are humans who fell into the void and took 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 slave who was turned into a monstrously powerful Energy Being that lost any and all traces of humanity a long time ago thanks to a botched ritual.
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.
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.
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 Legend of Zelda: Spirit Tracks has the fittingly named Skeldritch, a giant, humanoid, ancient demon skeleton thing with an unusually large spinal column, and wearing spiked viking attire. What exactly was this thing? Was it ever even alive at one point?
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. Which, by extension, would make Demise's Reincarnation, Ganondorf, a Humanoid Abomination.
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 vacuum cleaner! The Negativitron travels the cosmos, constantly sucking up all material in Craftworld. It can also be considered an Eldritch Location, too.
The object of The Lobotomy Corporation is to run a facility dedicated to containing, studying, and extracting energy from, multiple monstrous creatures. Oh, and if you don't keep their moods just right, they'll escape containment and go on rampages throughout the facility.
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.
Minecraft: Story Mode: The Wither Storm, made by substituting one of the soul sand for a command block. Its mere existence breaks the world. Starting off as an average Wither, it goes One-Winged Angel, looking less like its original shape and more like something from H.P. Lovecraft, sprouting Combat Tentacles, growing to ten times its size and eventually becoming a distorted, black mass of destruction and death. It gets even worse in Episode 3, where it turns out to be an Asteroids Monster.
In Monster Hunter: World, the Final BossXeno'jiva is an alien Elder Dragon that is implied to have been birthed from the Sapphire Star mentioned in the Tale of the Five. Its glowing crystalline body, eight red eyes and blue flame breath all work to show how this creature is an UNHOLY threat to the entire world that must be dealt with.
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.
There's also the Black Goat, a beast said to be as "black as the space between stars" that lurks deep within a hole in an abandoned mine. Whenever he begins to sing, a cult kidnaps people off the streets and sacrifices them to him by tossing them down in order to keep their dying town alive and to quiet him.
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 Persona 2, we have Philemon and the Lovecraftian deity Nyarlathotep. Both are similar in nature and origin, in that they came from humanity's collective unconscious, with Philemon representing the "creative side" of humanity's mind, while Nyarlathotep represents its "destructive side". Naturally, the latter is the main villain. He also fits the trope straighter since Nyarlathotep can appear in physical world, and actually manages to rewrite reality as we know it at the end of Innocent Sin. His various forms, especially his Crawling Chaos form (this page's image), emphasizes just how different beings from the collective unconscious are when compared to the typical Personas or Shadows.
Persona 3 reveals a primordial goddess who existed long before humanity even existed, and actually helped to shape humanity's mind during the dawn of time by creating various Arcanas. She is referred to as The Mother, Death, and Nyx. All this time, Nyx hibernates within the moon, sleeping until humanity's mind become too clouded by self-destructive desires. If that happens, Nyx will be convinced that it's time for her to bring uponThe Fall to end humanity. Naturally, she thinks that now is the time, and sends her avatar as the Final Boss. As the heroes fight her to assert themselves as living beings (on the slimmest of chances they might even win), she then allows herself to be beaten as a courtesy to let the heroes live to their fullest, then shrugs off the defeat and continues to bring about The Fall. Ultimately, this fate is only averted when the Main Character receives an 11th-Hour Superpower courtesy of The Power of Friendship, and even that only manages to convince Nyx that it isn't the time to end humanity yet. Oh, and by doing so, the hero dies. She then hibernates again, until humanity's collective unconscious calls her again.
In the Updated Re-release, Persona 3 FES, reveals another one. They learn the existence of Erebus, a being from the collective unconscious, representative of humanity's unconscious desire of death. This thing is the real problem of the story, not Nyx - Erebus' very existence causes Nyx to try and end humanity. The hero dies not to seal Nyx away, but to keep Erebus from calling Nyx. However, Erebus is trying to fix that through the Abyss of Time, to rewind time, recall Nyx, and ensures humanity's end.
In Persona 4, many things from beyond the TV screen count, as does Izanami, who is another representative of humanity's collective unconscious, specifically the willingness to lie and desire to run away from truth. The fog from the TV world serves as a reminder of this, as it is toxic to normal humans and will turn them into Shadows through prolonged exposure.
The Persona 4: Arena series has Hi-no-Kagutsuchi, the collective will of those who abandon all connections, and strive to live only for themselves.
Persona 4: Dancing All Night has Mikuratana-no-Kami, the embodiment of the desire for an eternal, painless bond, even if said bond is false.
Persona 5 continues the trend with Yaldabaoth, the embodiment of the collective desire to maintain social order, regardless of the costs or actual morality of such actions.
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.
The entire setting of Prey (2006), 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 legends of Ryzom mention a Dragon whose breath created the Goo and who sleeps in the Prime Roots after having been beaten back by the Karavan. The legends go on to say that when The Dragon wakes up again, it will bring about The End of the World as We Know It in its death throes, killing any Homins left on Atys. The Fyros want to kill it, which irritates the Karavan to no end since their policy with the beast is "DO NOT TOUCH."
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.
Yog-Shoggoth, AKA Dr. Norrington from Sam & Max: The Devil's Playhouse, is explicitly stated to be an Elder God, and is built up to be just as mind-breakingly horrifying as any other example on this page. When we get to see him, it's a bit underwhelming. He's embedded in Paiperwaite's torso, and can do nothing but move his head and arms. Coupled with his gruff British accent and generally refined nature, it's not a very threatening sight. He boasts that his true form is much more terrifying, though.
Junior, the original "owner" of the Devil's Playbox, plays this trope completely straight appearance-wise, but his behavior more resembles a spoiled toddler than anything.
Maxthulu, the fused form of Max and Junior, is essentially a Kaiju version of Max with incredibly powerful psychic powers.
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.
In the Video Game Space Station 13, there is a cult that can summon forth Nar-Sie, the god of blood, that explodes anybody who comes near him.
Every demon is technically this, even those that resemble humans. They're masses of energy given thought and shape by belief (whether it comes from humans or otherwise, even other demons, really doesn't matter), from the lowliest Slime, to the highest deities of every pantheon.
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 its 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.
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.)
Starbound starts out with the destruction of planet Earth and the peacekeeping Terrene Protectorate by the enormous, skyscraper-sized tentacles of The Ruin, an ancient force of destruction and chaos that has been sealed away in a failing extra-dimensional prison since times immemorial. The final plot mission of the game transports you to The Ruin's prison and onto the creature's surface... and you're explicitly told that while it appears to be a planet, it is actually a planet-sized living organism.
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.
The Xel'Naga themselves. They are near immortal beings that come from the Void (or literally nowhere, a place between universes). They don't have any physical form until they enter a new universe, and when they gain a physical form, it looks like a gigantic manatee with tentacles (well, at least in our universe).
Sel Makor created the Voss species and grants them their visions. It is the living embodiment of their war with the Gormak and grows stronger with every death.
The World Razer, who the Rakata were so afraid off, they built an entire planet to imprison it. You have the option of releasing it.
The Sith Emperor gained immortality by absorbing all of the Force energy of a planet, to the point that the Force ceased to exist in its atmosphere, and plans to do the same to the entire universe.
The final boss in the Terror from Beyond Operation named The Terror From Beyond. It is a giant tentacled abomination summoned from a giant hyper-gate by the Dread Masters.
Sundered has Nyarlathotep, the Crawling Chaos. It is a vaguely humanoid, legless giant whose body is a mass of black tentacles wrapped around a glowing skeleton and whose “face” is an animated, disembodied mask of the lower half of a human face. The monstrous beings of the Eschaton are implied to be worshipping both it and similar entities from the Cthulhu Mythos. Its influence extends throughout the caverns where the game takes place, most visibly in the tentacles that emerge from patches of darkness in the Eschaton Holy City and the Cathedral, as well as the giant crystal formations that its avatar, the Shining Trapezohedron, uses to relate the history of the caverns to Eshe. It can resurrect the dead and grant supernatural powers to people through Elder Shards, a process which gradually corrupts them into its monstrous slaves. But for all its power, it is trapped in the caverns and wants to get out.
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.)
Super Robot Wars Z3: Hakai-hen reveals what exactly this is. The Supreme God Z, a large angelic being that has existed for countless cycles, is responsible for creating and ending the universe, and is so powerful that the corpse of its previous incarnation, Sol, has reality warping powers.
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.
Thumper: The Omega Boss seems to become more and more like one of these all the time, getting spikier, more deformed, and more tentacle-y each time you face it, until it's more like a giant, flaming, metallic anemone than like a burning, screaming human head. Also, its true form is implied to be a large inexplicable triangle that serves as a phase of the boss fight.
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 Afterblank 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.
Flowey, after absorbing the souls of Asgore and the six fallen children. In a world where battle sprites are monochrome and pixelated, he appears as a multicolored, photorealistic meld of flesh, plant and machine, capable of generating bunker buster bombs and finger guns en masse with a thought. Oh, and he weaponizes Save Scumming.
And especially the Amalgamates, which are actually nothing more than normal monsters from the game...but fused and melted together into horrifyingly grotesque and disturbing new forms as a result of Alphys' tragically failed Determination experiment to try and find a way to get monster souls to persist after a monster's death, in hopes of gathering enough of those to break the barrier with instead of waiting for more humans to fall down. Literally the only thing uglier than their appearances is their origins.
Warcraft III 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. (Although they may shout a little too loud here.) 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, the mantid 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 (being mindless helps protect against losing ones mind).
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 in Cataclysm, 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. They are empowered by, and evoke, their respective emotion in others - the largest one, Anger, is the size of a tall building, and serves as a world boss. They are the remnants of a dead Old God, the dying curse of the seven-headed Y'shaarj who was killed by the Titans long ago.
With the release of the World of Warcraft: ChronicleAll In The Manual series, it's revealed/retconned that the Old Gods are manifestations of the Void, one of the basic forces of the universe; the nasty one, apparently a kind of actively malicious nothingness. Presumably all Void creatures are pretty eldritch, since this is what they embody. The Old Gods were sent by the Void Lords (or "Void Gods") to corrupt worlds in order to corrupt a Titan that hasn't yet "hatched" from the planet housing its soul and create a Dark Titan — an overwhelmingly powerful being that would bring the entire universe under the power of the Void.
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.
One Bonus Boss, Tartaros, is described in-game as something so evil that its mere presence in the physical world blights the land, and it took an entire city of fairies just to seal it away. Link finds it in a "cocoon" resembling the Wind Fish's egg, but covered in veins and bloody eyes. It can be defeated, but it's widely recognized as the most difficult boss ever scripted for Zelda Classic.
The Big Bad, Venser, also qualifies. He's a dead "false god" from another dimension who's trying to collect the Triforce to be reborn and return home. Unfortunately for everyone else, the latter involves recklessly tearing through other dimensions - including Hyrule's - and causing them to collapse. His true form wouldn't be out of place in a Lovecraftian setting.
The Nexus Clash pantheon has Ahg-Za-Haru, an unknowable, mindless singularity of pure hedonistic selfishness and Tholaghru, a world-sized, slavering and utterly insane chaotic god-being responsible for most of the setting's Body Horror. Tlacolotl, the third evil member of the pantheon, is all too human.
Warframe has the Sentients, who were originally created by the Orokin but returned from outer space as an extremely powerful force hellbent on their destruction. The Sentient Hunhow is the most powerful being known to the Tenno, and was easily able to outsmart The Lotus who actually turns out to be a rogue Sentient in humanoid form- Hunhow's daughter Natah, in fact. Sentients can interfere and distort technology and warp themselves to become resistant to any attacks. They are significantly smarter and stronger than any of the standard races. Other than The Lotus none have been seen in person, as they prefer to manifest largely as pure energy controlling machinery to form abstract shapes. They were almost able to defeat the Orokin, an immortal race of near-gods, until they were beaten back by the Tenno. They're only weakness is void energy, and by extension the Tenno who can wield it.
The Secret World features the Dreamers, the creators of the Filth. And by the way, that name isn't a coincidence: not only have they been slumbering for millennia and kept asleep through the power of the Gaia Engines, but the Filth itself is their dream of awakeningmade flesh. Events throughout the game are orchestrated by them from behind the scenes, with numerous eldritch races of monsters having been engineered through their influence and countless historical figures having been seduced to their service - all without ever wakening from their sleep or escaping from the Gaia Engines. At no point do you ever get to see what they really look like, and you never once get to fight them - because they're too powerful to be fought. These things eat stars and dine on quantum foam. If one of them were to ever rise from their sleep, it could end the world in a matter of minutes. How do we know this? It's already happened. See, the Gaia Engines have been able to harness the Dreamers' power in order to turn back time and avert the apocalypse, but it's come at the cost of leaving the world reset to factory settings. And after four consecutive resets, the Gaia Engines are starting to break down and might not be able to reset things again if the Dreamers wake again.
Vampyr: The Red Queen, the progenitor of vampirekind is an ancient entity that used to be revered as the goddess Morrigan and now currently slumbers in deep sleep. That said, when she awakens bad things happen. To be specific, she awakens every few centuries to punish mankind for its inequities by unleashing plagues and calamities upon the land such as the Black Death and the Spanish flu, which takes place during the game and makes her the game's Big Bad. At the end, the main protagonist has to defeat her to stop the plague, but he only fights against her avatar as the final boss and when beaten, she agrees to go back to sleep so she can return in a few centuries to start the whole process all over again. Her son Myrddin on the other hand qualifies as an heroic Eldritch Abomination, since he is a being just like the Red Queen, but devoted in protecting the land (albeit he is very detached from humanity and unable to act directly).