The World Without The War has the Four Elemental Beasts, who were created by the World Spirit before it took notice of humanity's existence. Their "logic" is similar to that of the Avatar, and when the Phoenix, the Beast of Fire, escapes, the other three Beasts will awaken, they would destroy civilization. Because that's the only way they can communicate with humans.
Invoked/parodied in Operation: There Is No Operation where we meet the Galactic Kids Next Door, some of which are eldritch abominations with unpronounceable names. Since they are minors, they only induce temporary insanity in other species who see them and only with specific intervals, so as long as you remember to blink at the right time, you are fine. Oh, and one of them wants to date Nigel Uno.
Happy Families Are All Alike has mentioned unliving beings from beyond the veil of death (which Orochimaru apparently enjoys killing) and the Kyuubi has displayed unnerving powers, which in the 7th chapter escalated to full-on mind-shattering Eldritch Abomination status.
The Ranma ˝/Sailor Moon fic The Dark Lords Of Nerima has something called Unit Zero. We know next to nothing about it, except that it has enormous power and if given the chance, will attack Sailor Moon via some unknown means.
The fan mod Blue Planet applies this to the Shivans (who were merely Starfish Aliens in the canon games... as far as anyone knows). Shivans in the BP-verse are implied to be tied to the very fabric of reality, and are eternal, infinite, and (as a whole) invincible. They are also described as being "as far above humanity as humanity is above a protein chain". Much of exactly what they are is obscured through some very strange Techno Babble, for example, they were described as not being "made" but rather "calculated". Being in contact for a brief few minutes with the Shivan consciousness contains a real risk of the human going completely insane from the experience, and several times Ken deliberately cuts off contact to certain parts of it to protect the player's mental stability.
Deathly Hallowed portrays Death as this. Lily summons it to make a bargain with it. She'll return it's cloak in exchange for Death protecting her son. However, even after using a ritual to allow it a form, it's described as having "Far too many hands, too many eyes, too many mouths" and can only seem to speak in a almost mind-raping form of telepathy or Black Speech.
Perhaps worse is all the Eldritch Abominations that seem to be after both Harry and Death.
Merely a Mare has Luna casually mention that she and her sister are more than four hundred million years old, spending most of that time playing in the glaciers and lava flows of the planet respectively, and the mane six are continually reminded that the two are very much Other.
Speaking of the Pony POV Series, it also has Discord's parents Entropy and Havoc, respectively the Anthropomorphic Personifications of Heat Death and Mass Hysteria. The former is so massive that her just rising from the ocean of chaos she calls home creates waves that could drown continents, and if she merely says someone doesn't exist (at least, in her own realm), then they never did. The latter is described as every fear that ever has, does, or ever will exist personified, and is so horrific to behold that just looking at him will leave a mortal pony incapable of sleeping for the rest of their days at best. Entropy erasing Havoc from existence, then him willing himself back into it is equal to one member of a bickering couple shoving the other. Both have severe Blue and Orange Morality, Entropy viewing nothing as of value (even her own children) while Havoc's is described as, while valid, so alien its impossible for the personification of Wisdom to put it in words a mortal can comprehend. Meanwhile, Celestia's parents are just as massive, powerful, and indescribable, but are among the kindest beings in existence, even stepping in and saving the pony world from Havoc and Entropy's wrath when they were accidentally enraged and being in the presence of either is described as reassuring and pleasant. The Father of All Alicorns is stated to be Pony Heaven. All four Elders are multiversal singularities, meaning every alternate version of them is merely another part of the same being.
Discord's repeatedly cameoed cousin Ponythulu, who seems to be this trope played for laughs, as he's yet to do anything remotely evil, and actually seems downright friendly.
Nightmares tend to have traits of this, but the "Super Nightmares" (who have managed to mutate somehow) fit it to a T. Nightmare Whisper is a gigantic, vaguely dragon-like monstrosity with a burned and blackened hole in her chest and exposed with an undead foal inside due to sucking all of Equestria's sins and evil into herself (trapping all those effected in a Lotus-Eater Machine or reducing them to a foal) and obtaining the Elder Horn. Nightmare Mirror is an equally huge Multiversal Conqueror with wings covered in eyes who can force the victim to witness the harshest truths about themselves if they look in them and is described as having a constantly shapeshifting form. While Nightmare Eclipse/Paradox has a lot of traits of one, she leans more towards being a Equineoid Abomination, though one of her Psycho Rangers, Nightmare Banneret (Spike's Nightmare) resembles one.
By the time of the Final Battle between Shining Armor and Makarov, the latter has mutated from a mere Equineoid Abomination into one of these; merely glimpsing its true form nearly causes Shining's mind to shut down.
King Sombra is presented as one in the brief Origins Episode Alex Warlorn gave him after finally watching Season 3 — he's the embodiment of the crystal ponies' collective fears, which they were tricked into purging from their hearts by one of Discord's cousins (who themselves count) in the belief that this would grant them further protection from Discord. Instead they got a monster whose every act was literally everything they ever feared would happen to them. And then, he developed full sentience...
In Under The Northern Lights, Luna's and Celestia's greatuncles and greataunts are described in a vision as "lights... sounds... patterns of magic in a black sphere that itched the brain and made the soul cry". They decided the laws of nature, seemingly on a whim. The only hostile one seems to be Discord, though, and his reality warping powers are presumably because he never agreed to what his siblings decided. The generation of their parents has some traits of eldritch abominations but are more like Our Titans Are Different, having motivations similar to mortal ungulates despite their ancient age, huge size, and inequine shape.
The Stars Will Aid Their Escape just cuts to the chase and outright crosses over with the Cthulhu Mythos. Therefore, the Big Bad is a stallion avatar of Nyarlathotep who hides his face behind a mask, as seeing it causes the viewer to go insane which is what happens to Twilight; his Mooks are the Dark Young of Shub-Niggurath; and in true Mythos fashion, Trixie goes crazy after using the Neighcronomicon and seeing the Young for the first time.
Nightmare Phobia, the Big Bad of the Chaos Verse (an official spinoff of the POV Series), is made from the remains of Nightmare Moon's essence, and exists primarily in the collective subconscious of ponykind. And that's before she goes One-Winged Angel, at which point she becomes a sentient void, which consumes Discord's pocket dimension and nearly emerges into the real world, which causes every living thing extreme pain.
Of all things, even Moonstuck gets in on the act with Discord. He uses an Enemy Without and a personification of depression as his puppets, drastically distorts and at one point shatters the fourth wall and the narration, and whose speech and appearance are very similar to the Anti-Spirals (probably deliberately, as the author is a fan).
A Future of Friendship, A History of Hate: The Sentiox came into being billions of years ago (and have since moved on to another plane of existence), came in a vast variety of forms (some rather normal-looking, some... not), and were powerful enough to create worlds... or in the case of Ruinate, easily destroy them. And speaking of Ruinate, he's one of the more otherworldly-looking Sentiox, being a large, vaguely frog-like creature, with three red eyes with cat-like slits, surrounded by (and possibly made of) a miasma of dark energy.
Parodied by the Reading Rainbowverse version of the Shadowbolts. They're definitely eldritch, and they can only be seen by Lightning Dust... but they only irritate her instead of driving her mad and the worse thing they've done is draw a penis on her forehead.
Nightmares Are Tragic: This is true not only of the villainous and extradimensional Night Shadows, but also of all Cosmic beings in our own Universe, including not only the Draconequii but even the Alicorns. The Alicorn Avatars in which Celestia and Luna incarnate are A Form You Are Comfortable With.
The Tears Of Gaia has The Blight, a sentient corruption in the form of a black cloud that turns anything exposed to it into twisted, monstrous versions of themselves, driven by a desire to corrupt or kill others. And as shown in the opening Creation Myth, it was even capable of corrupting gods, as it turned Discord and the other Draconequii from benevolent caretakers of the world into monsters out to destroy it.
For that matter, the Draconequii and Alicorns themselves probably count, being nearly as old as the universe, with their physical forms being A Form You Are Comfortable With designed to let them walk among their creations. Celestia and Luna are actually weak compared to their siblings, having given up their divinity to live directly with their subjects.
There's also the... thing in the dimensional rift where the Tears of Gaia were stored. We don't get a good look at it, but it's large enough that Twilight and her friends mistake one of its eyes for amoon initially, and the sound of its voice nearly deafens them.
Black Queen, Red King has at least three: Rex, Queen Chrysalis,note Though it's only their souls that qualify. Rex's soul has been described as "[his soul] glowed with a blindingly bright darkness." and Death/Chaosnote Not the same as Discord.
Ayanami Rei's Nobody Dies incarnation is this. And then there's Go-kun's left arm, which he brought back from the Aeon Natum Engel verse. The Angels, bizarrely enough, are a bit less Eldritch than they were in the series, due to actually having characters, motivations, and bothering to communicate with the heroes. Even then, constructs like whatever the hell 02-Ef A9 becomes still count.
''Persona 4: Five Years Later'' has Amatsu Mikaboshi, a sentient void without a self-identity, instead referring to himself as "the entity", a barely-sentient but very intelligent incarnation of the Void that existed before time, utterly devoid of human influence. Souji can only classify the Amatsu as pure nothingness, and Igor describes it as similar to Nyx.
The Forceless Collective in the Star Wars: Paranormalities Trilogy is an entire faction of these from another galaxy. Not only would Force-sensitives sense something off the light-dark spectrum of the Force from these things, but they are disconnected from the universe by being a dead spot in The Force and are implied not to be natural forms of life. Their primary symbiotic form, the Black Matter, is not unlike Mnggal-Mnggal in the Literature section. Unlike Mnggal-Mnggal however, the victims it possesses are still alive and conscious and can live for as long as several thousand years. If the host gets along with the symbiote, everything goes fine for the host, but if not, they lose control of their bodies while they still have access to their senses. (and Forceless are usually pretty ruthless). The creatures they possess also get mutated in the process of symbiosis, and some of them, particularly some of the Archfiends, qualify as abominations themselves.
As revealed in Movie 1 of Clash of the Elements, Pandora, the dragon trapped within Subspace, is one of these, and it is said that it has the capacity to be able to drag an entire world into Subspace if it were to ever fully emerge from a Subspace Orb. It is also stated to have a rather netherworldly glow around it...
In the Team Fortress 2 fandom, use of Garry's Mod had created multiple popular freaks. The most popular and well-defined are dubbed (in no particular order) Painis Cupcake, Snyphurr, Dic Soupcan, the Odd Scout, and Vagineer. Painis Cupcake twists his body in ways that will instantly kill or disable a normal individual, and is a morbid cannibal who seldom says anything except "I am Painis Cupcake! I will eat you!". Snyphurr is a giant torso with a concealed, bloody head; he turns people into stone. Dic Soupcan floats, mumbles irritatingly, and has multiple Gran-Mal seizures and will regurgitate explosives if agitated. The Odd Scout is distorted past even Slender Man proportions, converts other Scouts into its own distorted likeness, and can make Your Head Asplode through eye contact. The Vagineer is the original, and probably the worst, speaking only backwards and with powers ranging from using body parts of others to repair itself to corrupting others by its mere presence.
Imperfect Metamorphosis has the delightful being known as the Shadow Youkai. Walking Wasteland personified, a single touch can result in death, even the most powerful denizens of Gensoukyou are not completely immune from its corruptive power, in addition to its formidable combat abilities. Near-impossible to kill, its vanquishers could only seal it in a weakened from and strip it of its memories, but that didn't last long. And now, obtaining the resistance of Rin Satsuki and the immortality of the Hourai Elixir, even the combined forces of Gensoukyou may not be enough to stop it in time.
The Shadow Youkai is a Fallen Angel, fine. Yuuka, however, is an actual Outer God. As in, the Lovecraftian god-things.
The Plot Hole from PRIMARCHS. A living gestalt of all the plot holes accumulated in fiction that wants to eat the universe until only it remains.
Warhammer 40,000 has no shortage of this trope, but The Shape of the Nightmare to Come adds even more. The New Devourer is an unstoppable tide of death and hunger that eats a third of all life in the galaxy before inexplicably leaving, with hints that it ate everything in another galaxy. The Star Father is the God Emperor made manifest in the Warp, the Chaos God of Order that removes all thought and emotion in its subjects, and is so powerful that it took all four of the other Chaos Gods attacking it at once to prevent it from crushing them. Almost nothing is known of the Ophilim Kiasoz except that it causes entire star systems to cease to exist simply by being near them. And then there's the Nex, an Ultimate Evil at the (maybe) heart of the Warp. To Go Mad from the Revelation is the least terrible thing that can happen to you if you learn anything about it beyond its name.
The sequel, The Age Of Dusk, adds Draziin-maton, apparently Pre-Fall Eldar constructs possessed by... something, from layers of Warp so deep that their presence alone turns Daemons into unfanthomable, mindless chaos.