After God: Each IPO's true form is weird, but Alula's is completely incomprehensible and can be described as "fractal flesh flower drawing" due to having cells of other Gods.
While their true physical forms may be incomprehensible, they are psychologically much closer to human, to the point where god-human romances are common enough to warrant the creation of a heavenly "Inter-species Romance Department". When properly managed, these relationships can be incredibly loving and fulfilling for both parties. They may have the bodies and powers of eldritch abominations, but at heart they're not so different from regular people, a belief Keiichi himself expresses near the end of the manga.
The titans would better fall under Humanoid Abomination, but the nature of the power behind them—regeneration, nimbleness despite their gargantuan sizes, and the ability to manifest flesh, bone, and sinew from seemingly nothing, among other things — are extremely alien, making it nearly impossible for our heroes to understand and combat them. However, one titan truly embodies this trope: Eren Yeager's fully-realized Founding Titan dwarfs the Colossal Titan and even Rod Reiss' unusually large titan form in size, is made up almost entirely of bones, and doesn't look anywhere close to a human, instead more resembling a dinosaur or a caterpillar with how it walks with its ribs. His abilities in this form are also eldritch: he can flatten an entire continent in a few days with his control over thousands of Colossal Titans; summon an army of intelligent titans from the past; and finally has complete control over all Subjects of Ymir, being able to send them to an ethereal plane of existence, and can mind control, memory wipe, or even sterilize them.
The unnamed... uh, thing that appears to be the source of the Titans. It's also described as the "source of all life" and "the source of all organic matter". It somewhat resembles a disembodied human nervous system or perhaps a hallucingenia, a type of extremely ancient sea worm. In the end, NOTHING at all is explained about this thing; a slave girl just randomly happened to encounter it underneath a tree, it bonded with her spine, and she became the first Titan, as well as the progenitor of the Eldian race. It is somehow able to bond itself with up to nine humans at once, seemingly passed on through a combination of spinal fluid and genetics.
The Apostles. Former-human beings who made Deal with the Devil that is the Godhand members, they are capable of switching between their relatively human forms and their Apostle form. Their Apostle form represents the forms of their souls within the Astral realm, and bring it forth into the physical realm. Despite their often unnatural and hideous forms though, they are nowhere as reality-breaking as the Godhand, and is relatively just powerful physical monsters. Emperor Ganishka however, does qualify when he reincarnates himself into a tentacled giant who resides between the physical and Astral realms, whose size dwarfs a whole city and can function as a bridge between the two realms. As a side-effect, he also becomes mindlessly destructive and spawns innumerable lesser abominations to kill and eat everything in their path.
The "sea-god" is an obvious Cthulhu Expy, and possibly the most powerful non-Godhand-related entity seen in the series to date; humans it consumes become tentacle-like extensions of itself that can stretch for tens if not hundreds of miles, and when Guts enters its body to kill it by destroying its "heart", he is assaulted by its spiritual presence, deafening heartbeat and terrifying hallucinations of deep-sea life that nearly overwhelm both him and Schierke (who is piggybacking him in astral projection to guide and empower him at the time).
Raphaello from B't X is a homebrew version of this: amorphous, constantly growing, Nigh-Invulnerable, and assimilating everything in its path.
The Destroyer. Born from the Fusion Dance of two powerful beings, it has no sense of self or even attachment to life and expelled all of its emotion when it awoke, which was described as "life itself spilling out" by one of the spectators. Its true form is a black, shapeshifting tar-like mass of bodies that sucks out the life from anything it touches, and its energy is described as otherwordly and overwhelming. It also shoots things that either infect those they hit or turn into monsters.
Priscilla, the strongest damn thing in the whole setting. In 3'rd Extra Chapter Rigardo, by observing Priscilla, came to realize that her physical body (including her demon form), as absurdly powerful as it is, is little more than a shell that merely contains an infinite chaotic raw power waiting to be released. On rare occasions when we see her damaged a mass of deformed tentacles pours out from the wound to devour everything in their path before reforming as the missing body part.
The Dark Queen and I Strike Back has Anomaly, a pair of twins who were once Seed Eight's experimental specimens. They were given a Divine Craft that allowed them to shapeshift, but lost their minds as a result. When Seed Eight decided to dispose of them along with many others, the twins absorbed the other specimens and became an enormous, grotesque monster with a potent Healing Factor. Anomaly continues to absorb people to expand its mass, with no regard for friend or foe. Notably, Anomaly seems to no longer be a living thing in the conventional sense, as Fleonell's first Arcana (which affects living things) is unable to revert its body.
Death Note: The Shinigami King; in Death Note 13: How to Read, all his statistics are given as inapplicable, unknown, or immeasurable, and his portrait is replaced by a text saying "Incomprehensible." In the artist interview in, Takeshi Obata says he was too scared to think of designing his appearance. However, a brief flashback in the manga does show him looking quite eldritch◊.
The D-Reaper from Digimon Tamers, a data-disposal program that got plugged into cosmic power. To fulfill its objective, a null-state for everything, it mutates into more and more alien forms, all inspired by the Cthulhu Mythos (mixed correspondingly with designs of the Angels from Evangelion). Unique in that it gets worse when it becomes aware of humans as entities; it taps into the agony and pain of one little girl, amplifying and becoming The Heartless and quite, quite insane by anyone's standards. It is both artificial and technological in origin, which is extremely rare outside the franchise, and unlike other franchise examples is most definitely not a digimon itself.
Guilmon's Mega form, Megidramon◊. Guilmon starts off as friendly, but his Mega form is such an abomination that its very existence can tear the digital world.
Apocalymon from Digimon Adventure, a twisted mutant whose body is attached to an enormous geometric planetoid, and is composed of the data of Digimon who died failing to digivolve. He also seems to reside outside the Digital World proper (coming from beyond the "Wall of Fire") and his very presence in the Digital World warped its flow of time and also causing the creation of powerful evil Digimon.
The Digimon Adventure 02 episode where Kari gets taken by some Scubamon to the Dark Ocean is a rather obvious reference to the Mythos. The episode's climax reveals them to be digital lifeforms based on the Deep Ones. To top it off, the episode is named The Call of Dagomon.
Dagomon himself appears in Episode 64 of Digimon Ghost Game "The Call", a reference to the original Dark Ocean episode. Not only are humans outright betwitched and transformed into Deep Ones, a very real and berserk Dagomon can be seen hiding within the same large, black illusion seen in Adventure 02.
The virus-infected Cherubimon from the Supreme Evolution! The Golden Digimentals movie (or the final part of Digimon: The Movie, if you prefer) is an Angelic Abomination whose sheer existence warps space and is capable of bending time to his will. He is capable of regenerating virtually ad infinitum, and his insides are a chaotic pulsating mass of... something... filled with black spheres which represent the virus infecting him. Oh, and he's capable of appearing inside his own body somehow. Another one appeared in Digimon Frontier, but that one lacks these reality-warping powers and is thus significantly less frightening.
Quartzmon from Digimon Xros Wars: The Young Hunters Who Leapt Through Time looks less like a Digimon but an Angel from Neon Genesis Evangelion. He's also one of the very few villains who manage to take over the world and traps every single human being and Digimon he absorbed alive and in an And I Must Scream state, and at one point he gleefully manifests said humans and Digimon from his many limbs to invoke a Hostage Situation against Tagiru (again something that doesn't happen a lot with Digimon villains). To make things worse, there's no clear reason why he's even trying to take over the world, all of which makes a suprisingly dark villain for a light-hearted season and some of the most horrifying things in the series. His Digimon Ghost Game counterpart is a Well-Intentioned Extremist leading a mass excursion of Baby Digimon, but he's still very disturbing because he drops his clones and masquerades them as food, while said clones outright starve and malnourish their hosts and mutates their mouth and limbs to resemble his a while later. And the heroine finds herself becoming one of the victims.
Millenniumon's line is yet another. In particular, his final form, ZeedMillenniumon is explicitly stated to be an abomination with no desire other than to roam around and destroy entire universes. And whenever it appears anywhere, its intelligence and actual scope of harm may vary, but it's always taken seriously because it doesn't play around when it shows up. Special mentions to its Digimon Ghost Game counterpart who killed a woman and proceeds to roleplay the Thing inside her corpse with the sole motive of eradicating everything in the world.
The Ghoul from Divergence Eve, bizarre extradimensional maybe-biomechanical space monsters whose mere presence screws with space-time something fierce.
Dragon Ball: The anime-only Darkness is one of the most mysterious and disturbing beings in the early series. Residing in a deep dark maze-like cave in the land of ice, Korin doesn't explain what the Darkness is and only that its guarding the Ultra Divine Water so that only the worthy can drink from it. Darkness has no clear form and even has the power to send to demonic snowmen to attack Goku and Yajirobi on the surface and even more creepily Darkness can create illusions of Goku's friends and Kami House to try convince to remain in the cave forever. The simple minded Goku is fooled briefly and doesn't question why his friends are speaking in horrifying echoey voices, or why Kami House is sitting inside a dark cave. Goku escapes from the illusions and proves his worth by saving Yajirobi, this causes the Darkness to allow Goku to drink the Ultra Divine Water when offers it to him waking up Goku's latent power and gives him the strength to fight King Piccolo. The creepy part is the Darkness still lurks in below in the Dragon Ball World. On a side note, it appears to be based on the Umibōzu of Japanese folklore.
Dragon Ball Z: Majin Buu is one of the most mysterious villains of the series and the Dragon Ball equivalent to Void Termina. The heroes think that he's a weapon created by Bibidi, but they're wrong; he has existed since the beginning of the universe, and Bibidi just learned how to summon him. He can absorb whoever he wishes, is stronger than most gods in base form, and can only be killed if atomized- smoke is enough to regenerate him completely.
Zen'O himself is probably the best example: He erases entire universes that displease him, has the mentality of a child, and creates the Tournament of Power with the intent of destroying all the losing universes except not really, since the whole thing was a Secret Test of Character to see if all the universes were worthy of saving or destroying. In short, he's a serious version of Abridged Mr. Popo. It's a very good thing he's friends withGoku.
EDENS ZERO has an entity called a Chronophage. A planet-sized Spacetime Eater that can only be perceived as a strange mass of energy drifting through the universe, it feeds on the "time" of planets in its path, which effectively rewinds those planets to an earlier state. Any person who happens to be on a planet the Chronophage feeds on will either be replaced with a past version of themselves, and if they weren't on the planet at the time that it gets rewound back to, they will simply cease to exist. There is nothing that can be done to stop its advance or fight it off, and the only way to truly survive is planetary evacuation.
In Fairy Tail, Acnologia, the Black Dragon of the Apocalypse, definitely qualifies compared to what we know of other dragons. The gap between it and human beings is so immense that communicating with it to fathom its thoughts is completely impossible even though it's fully capable of understanding human speech.
Zeref: In spite of that, the reason it doesn't use words is because it doesn't think of humans as anything more than insects. You wouldn't stop and talk to a pest buzzing around you. It's the same for the dragon. You also wouldn't bother taking an obnoxious insect seriously even for a moment. There are things in this world that you cannot oppose or fight back against, no matter how hard you try.
The Gate of Truth, which is a giant floating Necronomicon with a giant eye inside that spews black tentacles and that gives eldritch lore in return for sacrificing your limbs or others' souls. It's guarded by a being that calls itself the Truth, which appears to be nothing more than an empty white void in the shape of you... Unless you go through the gate and are forced to pay a toll, in which case he begins to fill himself in with your stolen body parts. Every time Ed sees The Truth, it has his arm and leg. Add the constant too-wide grin and he's unnerving in his own way.
Some of the Homunculi, particularly Pride, when he isn't masquerading as a little boy, is a colossal mass of shadows filled with eyes and mouths, often morphing into innumerable Combat Tentacles, that could only be damaged by essentially straining him through the Gate of Truth. Gluttony as well, being a "fake" Gate of Truth, essentially a black hole that can suck in an infinite amount of matter (there's a reason he's hungry all of the time). Envy seems to be this, with a One-Winged Angel form that resembles a huge chimera covered in the screaming faces of the people who make up his Philosopher's Stone, although his true form is small and pathetic.
Their creator, Father, even more so. He originally looked like a black blob with eyes in a flask. Then he got a copy of Hohenheim's body that was actually a living Philosopher's Stone made of hundreds of thousands of souls. Then he turned into a living blob of shadow covered with eyes and mouths that assumes a mostly human form. Then in Chapter 104, after activating the nationwide transmutation circle and absorbing the souls of everyone in Amestris, Father transforms into an immense, nightmarish creature, which he uses to rip the Gate of Truth from the sky and cross the Bishounen Line to become a Physical God.
Getter Robo: A Humongous Mecha work of Ken Ishikawa gave us another eldritch abomination. It is immensely powerful. Its sheer size dwarfs planets. Its mere passing destroys worlds. It is told it is able to devour a whole universe. One single beam from it can blow to cosmic dust a planet and its fist can crush tears in the fabric of time-space. Vast armies and armadas have tried destroying it, only to be easily obliterated in turn without even managing to damage it slightly. Its name? Getter Emperor, the final evolution of Getter Robo. The narration goes as far as to state: "The voice that quakes the universe itself was indeed that of Ryoma Nagare".
Taken as canon, the axed manga that would happen in between supplies plenty of reasons for the sequel's scenario. If the creatures so far are mere space antibodies, then the Great Attractor turns out to be the conscious will ofthe universe. Being able to crush star systems with a thought is bad enough, but its body exists on a higher dimension that humans and their technology cannot perceive through. And it has long ago shed that to become God knows what.
The manga Hakaiju appears to be a condensed collection of different alien atrocities wrapped together in one Cosmic Horror Story in the form of a mysterious earthquake that leaves high school basketball player Takashiro fighting for his survival. The first chapter has the unlucky protagonist encountering what is a writhing mass of alien, three-fingered hands with biting mouths at their tips are only appendages of one of the least menacing ones.
Handyman Saitou in Another World: The Dark Spirit summoned by Primas manifests as a large pillar of fleshy stone covered in eyes that can shoot powerful destructive beams all around it, giving it incredible offensive and defensive capabilities; it takes the combined efforts of both Saitou's party and EVERY OTHER ADVENTURER THEY MET as well as TWO of Morlock's trump card magics and a rare moment of lucidity to barely defeat it.
Heavenly Delusion has the “Man-Eaters,” giant monsters of varying appearance such as animals and insects who devour humans in a post-apocalyptic Japan. They are also armed with supernatural powers such as freezing people and invisibility to help them hunt their prey down, plus many are shown to be intelligent, but the worst part is that it’s unknown if they even need to consume humans for survival.
It's clear that Alucard from Hellsing is just Eldritch Abomination/God-Vampire when he reveals the reason he is so powerful is because he has the blood of every single person he's drunk from, which powers him up to Physical God levels. When Alucard releases his familiars it comes out like a bloody and sentiment ocean. The only subversion comes from the fact deep down Alucard is a essentially a Tragic Monster and still remembers when he was human.
Heroman has Vine Monsters in one episode that seem to evoke this trope; as it turns out, the Vines are of Alien origin and a part of the Big Bad, Kogorr, who is himself an Eldritch Abomination when he's gotten the spheres he sent back to himself; he's also eaten several worlds, and we're shown the worlds he had consumed.
In JoJo's Bizarre Adventure: Golden Wind, the Stand Notorious B.I.G. definitely qualifies. Birthed by the hatred of its user, Carne, Notorious B.I.G. is a growing blob-monster the color of raw flesh that attempts to destroy and consume anything that moves. The heroes only stop it by dropping it into the ocean, and heaven help us if it ever reaches land...
And then, from the same season, we have Chariot Requiem and Gold Experience Requiem. Chariot Requiem is a soul-swapping, Stand-controlling juggernaut that mutates the bodies of every living thing on the planet, and its user has no control over it at all. Gold Experience Requiem is more controlled, but only comparatively, and it has a mind of its own and powers beyond the knowledge of even its user.
In Jujutsu Kaisen, most of the cursed spirits, including the likes of Ryomen Sukuna, are depicted as grotesque and terrifying monsters. Although some of them approach Humanoid Abomination territory (e.g. Sukuna or Mahito), they also originate from the human subconscious, since cursed spirits are formed from negative human emotions such as pain or envy.
Knights of Sidonia: The Gauna are massive, shapeshifting fetus-like creatures with with their extendible, prehensile Combat Tentacles. No-one knows where they came from or what they want, and their only apparent goal is to assimilate humans, giving them access to that human's memories and appearance. While their outer "placenta" bodies can be injured, Gauna are only able to be killed if their True Bodies are destroyed, and become capable of replicating the technology used by the humans.
Magical Girl Lyrical Nanoha A's has the Darkness of the Book of Darkness, an immortal, dimension-hopping, dimension-breaking, constantly morphing, bio-mechanical monstrosity that appears when you fill up all 666 pages of the Book of Darkness. If you manage to temporarily kill it, it will only rejuvenate in another dimension, where it will tempt another mage to fill up the pages of the Book of Darkness again, allowing it to be unsealed and go on another rampage. Magical Girl Lyrical Nanoha ViVid showed through flashbacks that, during the time of the Ancient Belka War when it was most active, doomsday cults worshipped it as a god. However, when we actually see her personality she's shown to be a Woobie, Destroyer of Worlds, literally. Her original programming was corrupted, and she can't control her own actions, making her a more benign example.
A rare mechanical, robotic version of this trope coming from Mobile Fighter G Gundam is the Devil Gundam (or the Dark Gundam depending on the dub). A Gundam designed to be completely autonomous and with no need for a pilot, and given the capacity for self-evolution, self-recovery, and self-replication, it's more akin to a giant Mechanical Lifeform than a Humongous Mecha. Given the resources, the Devil Gundam could build up its physical form at will, bordering on shapeshifting into configurations that look disturbingly organic. It could also infect people with "DG cells", with the progressing infection leading to influencing behavior, then possessing people, and even capable of overwriting them entirely. It also resurrected twice over the series. The kicker is that it was intended to help humanity (albeit not directly) by repairing and protecting Earth's biosphere, so that humanity could live there comfortably again. It decided that its main goal would be best achieved by killing off the humans (who were responsible for wrecking it) that remained on Earth, and preventing them from returning. In the series climax, it possesses an entire colony (not the people on it, but the colony) and intends to crash it into the Earth.
Naruto has the Ten-Tails, an ancient entity that possesses nigh-incomprehensible levels of power and can only be controlled by those possessing Wood Release. It has no feelings or ideals as such, its chakra can only be sensed in the form of the same natural energy that pervades the world. It also serves as the progenitor of everything in the Shinobi world and it’s a nearly unstoppable force of nature. It’s eventually revealed that its true identity, Kaguya Ōtsutsuki, merged with the God Tree to take the chakra of her own sons before she was sealed away and the Ten-Tails itself was split into nine pieces by the Sage of Six Paths who are all the Tailed Beasts of today and are also this but to a lesser extent.
In the Sequel Series, Boruto, it's revealed that there exists multiple Ten-Tails, and one of them is in possession of Kara. This Ten-Tails is smaller and implied to be much weaker, but it would still become a God Tree should it devour either Boruto or Kawaki.
Most of the Angels do qualify, being made of... something, have a human-like DNA, possessing barriers impenetrable to anything (and in some cases, can even become an entire sub-universe), but three in particular are noticeable. Leliel is an infinitely thin levitating disc that leads to Another Dimension, with a 3-dimensional shadow that casts its own shadow. Arael is colossal creature of light that can fire mind-raping beams from orbit. Armisael is a gravity-defying, double helix in a perfect circle that inflicts horrific Body Horror on EVAs and the pilots by attempting to assimilate with them.
The EVAs are artificial abominations. They can only be piloted by psychologically scarred children, and are the only things that can fight Angels. Their true nature as a clone of an Angel installed with a human soul is kept a secret until the end of the series, as they are built to cause Assimilation Plot involving Adam and Lilith below.
Adam and Lilith (the progenitors of the Angels and humanity respectively) are leagues above the Angels and EVA. The former's mere awakening killed off half of humanity and terrified the survivors so thoroughly they thought the EVAs were a good idea, and the awakening of Lilith, as seen in End of Evangelion, is such pure Mind Screw that it surpasses everything else seen in the series combined, and even screws with our real-life psyches. By extension, this makes Kaworu and Rei, the vessels for their souls, Humanoid Abominations.
The Rebuild films turned Ramiel, Sahaquiel, and Zeruel into this. Ramiel is now a living geometry that constantly morphs through impossible transformations whenever it is about to attack with a Wave-Motion Gun capable of melting mountains in one shot, constantly singing with inhuman voices and screams whenever damaged. Sahaquiel becomes (by Kaiju-standards) a gargantuan thing that mixes traits from three Angels of the original series, including the aforementioned Leliel. Zeruel takes the cake, for while it visually doesn't look any different, now it has at least 24 layers of AT-Field, can shoot off Eye Beams to one-shot a barrier that took Ramiel 10 hours to destroy, and can consume an EVA whole, and transform its body (but not its head) into a naked, human woman body to gain the traits of an EVA.
The Rebuild made the EVAs even more of an Eldritch Abomination. Unit-02 reveals a transformation with Body Horror that makes it several times more powerful and wild, and even grows a mouth to roar with. But that is nothing compared to Unit-1 and Unit-13, after devouring the core of an Angel, as both cause an apocalypse very similar to Adam's awakening above, if not worse.
The World of One Piece features a handful of shadowy figures that are so impossibly huge, they can stand in the middle of the ocean as if on land. First are the Sea Behemoths, immense humanoids that appear to be wearing some kind of armor and wield massive weapons, and the Florian Triangle monster. The former scared the Straw Hats to death to the point where they didn't even want to see what it was, which for them is very unusual. The latter is the largest creature ever seen in the series at around 54,000 feet tall. It's implied to be incredibly ancient and malevolent, as it's been destroying ships that enter its territory for hundreds of years and has glowing red eyes. While the Behemoths are implied to simply be the People of the Sky, whose shadows are reflected on the clouds and amplified, the latter's real identity is still shrouded in mystery.
In Psyren, the giant asteroid Ouroborus hides an amorphous, silvery entity which, upon the asteroid's destruction, spread to cover the entire world, causing a massive global storm which destroyed the entire planet and turned it in the bleak wasteland that's the world of Psyren, ruled by the evil W.I.S.E. lead by Miroku Amagi. It is later revealed that the thing inside the asteroid is a bona fide, planet-eating abomination called Quat Nevas, using the W.I.S.E. member Mithra as harald and manipulating Miroku and his life-generating Sephiroth Psi Power to gather enough energy to revive itself.
Witches exist as twisted abominations of Alien Geometries in their own chaotic dimension hidden and isolated from the rest of reality, crafting a realm and servants to carry out some nebulous and hopeless task, and having yourself touched by a witch will mind-control you into despair and suicide.
Technically magical girls themselves, the young, larval stage of witches. They look human, but that is simply a soulless shell they manipulate via remote control; their witch form is the true expression of their bodies and power.
Walpurgisnacht breaks the established laws of witches. It doesn't even need a labyrinth and can apparently yank skyscrapers into the air just for the hell of it. It took everything Homura could throw at it without a scratch, and in all the previous timelines defeating it was either impossible or came at a terrible price. Word of God is that is formed from a Fusion Dance of multiple witches.
Kriemhild Gretchen, the witch form of Madoka Kaname appears like a tower made of shadows with its top forming the shadows of a girl. With time, it will absorb all of humanity into its barrier. Since it grows stronger every time Homura resets time, by the time of the series, it is explicitly the most powerful witch ever, born from the magical girl that one-shotted Walpurgisnacht and its size had grown to the point it reaches the far sky, and would assimilate the planet in 10 days.
Ultimate Madoka is a benevolent example in the same vein asGod. She is less a being and more an abstract concept, referred to as The Law of Cycles, powered by "multiple universes" all centered around her in a singularity, and when she was born she deleted a law of physics and rewrote the multiverse, past present and future, to insert herself as a fundamental force of all universes, absorbing the full karma of existence's suffering to prevent Magical Girls who suffer despair from ever witching out and instead sending them to Heaven.
The end of Rebellion has Akuma Homura. She manages to break apart the Law of Cycles, takes Madoka's mortal self, then conquers existence and rewrites it to her designs as a paradise for herself and the human Madoka.
The Big Bads of the first, second, third, and fifth story arcs of Sailor Moon: Queen Metalia, Death Phantom, Pharaoh 90, and Chaos. Pharaoh 90 and Chaos are even closer to this trope in the first anime; the manga allowed them to speak at least, but the anime took away any human features, making them completely alien and unknowable.
Sgt. Frog: An enormous black hole dragon, composed by milions of smaller negative matter dragons, which appears in one of the show's final episodes (7th season), easily slaughtering the combined force of the Keronian army. Of course, the series doesn't end with it destroying the universe. So, somehow, it's defeated.
In the Shin Mazinger Zero series, it's the Mazinger Z itself, who seems to always lead to its creation of the rampaging titular Mazinger Zero.
The Great Old Ones are this or Humanoid Abomination in appearance. They're anthropomorphic personifications of madness of various kinds (i.e order/rule of law, terror, power, rage, knowledge). Asura is likely 'terror' and Eibon 'knowledge'. Shinigami and Kid are both 'order'. Excalibur represents Rage.
Kishin Asura, before he puts his skin back on. Also, Asura's superpowered, gargantuan form that he gets after he eats Arachne's soul. Fitting, as he IS the aforementioned Great Old One of the madness of terror.
Star Driver: Samekh. Sure, it's a Humongous Mecha, incredibly big even when compared to other Cybodies and scary looking, but that's far from being worthy the name of Eldritch Abomination, right? Well, it's of alien origin, sentient, and capable of resisting its Driver's will. It can destroy most Cybodies effortlessly, and those who are already broken can be resurrected as its slaves. It was sealed in Another Dimension by using four powerful Maiden Cybodies, and once it breaks free, it will consume Earth's entire life force, killing every single life form on the planet. It can also control time and space at full power.
The Noise from Symphogear - they have multiple forms, seems to be made of solid light, annihilate their victims by just touching them, are capable of combining, and the only thing that can kill them is Symphogear users, because they resonate with Noise, forcing them to obey the laws of physics.
The Anti-Spirals, having godlike powers, allowing them to break up laws of physics, create living battle ships as they want, create power-draining oceans in the middle of space, or trap people into a Lotus-Eater Machine at will, live in their own pocket dimension they created, create galaxy-sized Humongous Mecha at an instant, without using Spiral Power, and having very creepy forms, similar to a Living Shadow, with the Anti-Spiral King resembling a living chalk drawing. In a slight subversion, they are beings of order, or at least see themselves as such, and they were originally a normal race that evolved into an ultra-powerful Hive Mind.
The eponymous mech. It can only exist in a special space between dimensions, is impossibly large, and both it and the Grand Zamboa are able to weaponize galaxies. It's a giant robot that doubles as an Energy Being.
In Uzumaki, theruinsunder the lake are impossibly ancient, the sole force responsible for the curse of the spirals and all the insanity, mutations, and deaths (and worse) throughout the manga... And they have done so before and will do it again probably for as long as there is sentient life on the planet.
Yaiba has Princess Kaguya's true form, which looks like a colossal, black blob with many hydra-bunnyish heads and huge grins. Then there's Yamata no Orochi, who is an 8-headed, JAPAN-SIZED dragon that can erase whole countries in a matter of seconds.
Both the Orichalcos stones in the Doma filler arc, and the Light of Ruin that the Society of Light in Yu-Gi-Oh! GX's second season is built around, are Eldritch Abominations that were born from spatial phenomena and have no purpose but to doom the universe under their whims. Judai's Neospacians tell him that the Light of Ruin is a danger to all the cosmos.
Don Thousand's final monster, Imaginary Chaos Number 1000: Numeronius Numeronia, is one. It is a Rank 13 monster with 100,000 ATK, in a game where levels and ranks normally have a maximum of 12 and monsters with ATK higher than 4,000 are rare, and it has the ability to make the opponent automatically lose if they don't attack it.
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