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.
In Baccano!!, the "demon" summoned on the Advena Avis, Ronnie Schiatto, is heavily implied to be closer to this than an actual demon. He possesses phenomenal cosmic-scale Reality Warper powers, and his true form is so hideous, any who sees it immediately has their memories of it blocked. It's also implied that he Was Once a Man.
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 Invisible Thing" sealed insideTouma's right hand, which means woe to all who cut it off. It is so powerful, to the point that a conceptual being stronger than God is terrified of it, and nobody in the world has any understanding of what it is, except for a select few of individuals and divine entities.
The Enigmatic Empowering Entity contracted to Aleister Crowley, a top-secret existence codenamed DRAGON by the Academy City directors, a transcendent entity who calls itself Aiwass. Everything from the how it presents itself to how individuals perceive it emphasise how otherworldly it actually is. It nearly checks all the points of the trope:
When it shows up to confront Accelerator's group who are trying to investigate it, it instantly knocks them all out unconscious except for Accelerator himself, because it finds him 'interesting'. It proceeds to describe itself as an incorporeal existence which requires very careful applications of diffused AIMfields similar to the ones projected by Espers to manifest as an avatar of corporeal energy which requires further programming on Aleister's part to be shaped into a humanoid, tangible form with a prismatic core inside. The slightest miscalculation or interference on its programming would prevent it from interacting with the world, though it also says even if it is destroyed, it would return after 10,000 or perhaps 100,000 years, since it is not of this world to begin with. As it speaks, it occasionally speaks in gibberish as the human language cannot keep up with what it was trying to convey, which forces it to describe itself in a roundabout way. It also clarifies that calling it a 'dragon' or an 'angel' are some of the more accurate terms to describe it, even though both are not quite correct to describe its nature either.
In its next appearances Aiwass also displays shades of omniscience, as it knows about events happening thousands of miles away outside the AIM fields it dwells. In New Testament, Aiwass also displays the ability to exploit the theories people make surrounding its existence to manifest. As people theorise Aiwass is a type of 'extra-terrestrial life form' it allows him to partially manifest its avatar in outer space even without the AIM fields around to support it. It is also explained that Aiwass is essentially a life form from the deepest expanse of the world, beneath all the Phases which compose reality, close to the expanse untouched by magic which is why it's called 'the Pure World'. It has been summoned through Thelema designations as 'Holy Guardian Angel' and will play a vital role in Aleister's plan to destroy all Phases in existence to erase magic as humanity knows it.
Then, there are the Magic Gods, the highest position a user of magic could possibly attain, by turning oneself into a being capable of encompassing all 'possibilities' within the world. Othinus, the weakest known magic god, can instantly destroy the universe with a thought (or to be specific, she creates and destroys 'Phases' - the myriad of layers which make up reality, each can be considered universes on sheer scale) and instantly conjure a magic bow larger than Earth. True Gremlin, composed of the other magic gods, need to divise their powers trillion of times before they can go outside their Pocket dimension because their powers can wreck entire Phases simply by moving their arms.
The later parts of New Testament introduces more entities from the Aeon of Horus, which can all be considered Eldritch Abominations from the perspectives of ordinary people (Aeon of Osiris). Any one of these entities can take on Magic Gods one-on-one and expect to win: through summoning them from their planes of existence is extraordinarily difficult and exceptionally risky. One such entity was summoned by Aleister's former colleague Samuel Mathers through the Thelema designation 'Great Demon Coronzon', whom he had bound to a contract to torment and destroy Aleister's life. Despite being a Thelemic demonic entity, it doesn't reside in the Qliphoth as with all other demons but instead in the Sephiroth, in the Abyss of Da'ath, and its function is to govern over those who go up and down the cosmic tree (material and spiritual planes). Its nature is 'dispersion' which means its ultimate goal is to bring upon the natural dispersion and destruction of the elements which made up the surface world. To carry its purpose, Coronzon requires an avatar just like Aiwass: though the demon has prepared several humans across the world to possess as secondary avatars in addition to its primary one, Lola Stuart.
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.
Several Evil Gods from The Death Mage Who Doesn't Want a Fourth Time are downright alien to look at, like a giant hand whose fingers were replaced by one-eyed snakes, a bundle of tentacles arranged to look like a woman, a genderless arachnid made of Alien Geometries and so on. Many of them went through a HeelFace Turn several thousand years ago and now are allies of the protagonist.
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 mutated 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 got worse when it became aware of humans as entities; it tapped into the agony and pain of one little girl, amplifying and becoming The Heartless and quite, quite insane by anyone's standard. 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 started 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.
The virus-infected Cherubimon from the Supreme Evolution! The Golden Digimentals movie (or the final part of Digimon: The Movie, if you prefer), a psychotic mass of hate 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.
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 snowy mountain, Korin doesn't explain what the Darkess is and only says it's 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 Moutain's 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 echoes 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, it appears the 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.
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 Homonculi, 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? GetterEmperor, 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".
The Big Bad of Godzilla: Planet Eater and the Godzilla Anime Trilogy is Ghidorah, who in this version is a truly gigantic dimension-crossing organism made of energy that takes the form of a golden three-headed dragon whose necks alone are 20 Kilometers long. It's revealed that Ghidorah was pulling the strings ever since Godzilla appeared on earth in 2030, and that all the human-alien orchestrated event s(the emigration, the info dump on Godzilla, and the return to Earth) were all orchestrated by the Exif on HIS orders. When Ghidorah destroys the aratrum, it is shown that he can warp space and time itself, causing the crew to come the realisation that they're already dead. When Godzilla attacks Ghidorah using his atomic breath, Ghidorah easily bends the atomic breath away from him.
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 which, as later panels shows, are only appendages of one of the least menacing ones. And then there are creatures like this.
The Celestials are giant glowing blue manifestations of Haruhi's frustrations with the world. They appear only in her "closed space", and serve no other purpose than to destroy everything in the surrounding area. If left unchecked, the closed space expands, and could destroy the universe.
Heck, even Haruhi and Sasaki herself could be an example. An omnipotent god in the form of a childish young girl that doesn't realize she is omnipotent? Eldritch enough. Overlaps with Humanoid Abomination.
The Data Integration Thought Entity, Yuki's boss, is a non-physical data lifeform that exists outside of normal space-time. It lacks the ability to communicate with language, so it created Humanoid Interfaces to interact with humanity on its behalf. Its goals and motivations are unclear, despite Yuki's attempts to explain, only that it is interested in Haruhi Suzumiya. Yuki also mentions that any human who sees it would die of information overload.
Then you've got the Cloud Canopy Domain, a data lifeform similar to Yuki's boss, but completely alien and unknowable even to them. Their first attempt at a conversation involved trapping the Brigade in a pocket dimension, and they eventually create a truly alien Humanoid Interface that makes Yuki look like a perfectly normal Genki Girl. At least the Data Overmind's interfaces can pass for human most of the time; Kuyou Suou is so profoundly inhuman that normal people simply will not acknowledge her existence unless forced to.
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.
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.
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, was 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) 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.
In general Sea Kings are the abominations of the Sea and some don't even resemble fish; beating just one is mark of a super human. The even bigger Sea Kings deep below the ocean near Fish-Man Island are even more scary◊ (even Jimbei had a Oh, Crap! moment). Mermaid Princess Shirahoshi can control them, which makes her Poseidon one of the Ancient Weapons of legend.
The Lily Carnation from Movie 6 is probably the scariest monster in the franchise and there's absolutely no explanation to what exactly it is or where it came from other than being called a "a rare flower". In it's base form it's just a cute little flower with eyes and mouth that's seemly growing out of Omatsuri's shoulder but then it turns out the titular villain is the flower's host and his been feeding it pirate crews so it can produce plant-replicates of the his dead crew. The pure Nightmare Fuel comes in when the most of Strawhats (Zoro, Nami, Usopp, Sanji, Chopper and Robin) have been swallowed by the abomination and Omatsuri reveals it's horrifying true form◊. It's especially freaky when Baron Omatsuri uses the flower's power to reduce Luffy to a terrifying zombie-like state. Though the Lily Carnation is killed by a simple bow and arrow, it's nevertheless probably the most demonic and scary One Piece movie villain to date. Movie 6's writer Masahiro Ito is one of the creators of the Silent Hill series, which may explain the darker mood of the story compared the main series as well as the Eldritch Abomination in the aforementioned Lily Carnation.
Pokémon: Toned down some from the games' Pokédex descriptions, but some of the Pokémon remain delightfully creepy. A Notable case is the Creation Trio in the Sinnoh movie trilogy, Dialga and Palkia's clashing can send a small city to an pocket dimension as well as dissolve it into another dimension. Giratina lives in an Eldritch Location that looks and feels off (especialy with the wonky gravity) and Arceus is still the equivalent of God. Most of these overlaps with Animalistic Abomination.
Unown in Movie 3 are, collectively, the most impenetrably enigmatic force in the Pokemon setting. They barely look like Pokemon, no-one knows where they came from, what they want, why they look like writing, how they think, or how they combine their individually miniscule psychic powers to arbitrarily rewrite local reality, or even what the curve of Reality Warper potential looks like as a group of Unown gains members. Their name even comes from the word "Unknown", and the only move they can learn is called "Hidden Power".
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 Kaname Madoka 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.
The Noise from Senki Zesshou 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.
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.
Slayers features the Mazoku, a race of Always Chaotic EvilOmnicidal Maniacs serving the Dark Lord Shabranigdu, The Lord of Nightmares, who even the mazoku find incomprehensible and alien. Just to top things off, a semi-regular member of the group is Mazoku himself.
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.
Sukasuka: The 17 Beasts wiped out all life on the surface within a year of their first appearance, driving the survivors to floating islands just barely out of reach. Each subtype of Beast differs drastically in form from the others, but theyre all united in their burning hatred for all other life forms. While theyre all Eldritch Abominations, Shiantor the Lamenting First Beast is by far the most alien. Its powerful Reality Warper abilities and weird Alien Geometries, make it disturbingly similar to a Witch. No one has ever survived an encounter with this monster, so running is the only option if its in the area.
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.
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 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. Even Judai's Neospacians reminded him that the Light of Ruin was a literal 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.