While their true physical forms may be incomprehensible, they are psychologically much closer to human, to the point where god-human romances are (or at least, were before the introduction of the Judgement Gate) actually quite common. Romances which, when properly managed, can be incredibly loving and fulfilling for both parties. They may have the bodies and powers of eldritch abominations, but at heart they're still just people, a belief K1 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" from a recent arc 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).
Bleach's Soul King has been implied to be one of these since the Deicide arc. There's still much to be revealed, but he is almost assuredly this, since we've been meeting him as one giant, conscious body part at a time. Special mention is due the King's left arm, which is somehow a Quincy Sternritter, Pernida Parnkgjas. Unlike the other body parts we've seen, it has no humanoid form, just a cloak for a disguise. It's really a giant shapeshifting hand with eyes that talks in Hulk Speak. And it has countless invisible prehensile nerves that can take total control of objects and people — and even reproduce any special powers they have.
"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 maybe Aleister Crowley, and he's not telling.
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 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.
Majin Buu. This bizarre pink genie creature has terrorized the universe, cowed the gods themselves, can transform you into conscious food while eating you alive, or absorb you by using its own malleable flesh to break off and consume you as it reintegrates with him and transforms into a new form, taking some of the traits of the victims (this happened to God), and, sufficiently enraged, he can tear down dimensions.
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.
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.
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"
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.
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.
Il Sole penetra le Illusioni has the Daemonia, demon-possessed human beings that the magical girls must fight, and there's no way for them to defeat the Daemonia without also killing the possessed human. Most Daemonia are also fought in the Astralux, some kind of twisted facsimile of the real world.
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: The Ten-Tailsnote also referred to as the One-Eyed God, Daidarabotchi, Datara, or Shinju is so immensely powerful even the other Tailed Beasts consider it a monster. Like them it is formed of pure energy, but unlike them it lacks any emotion or ideals. The Big Bad's plan is to revive the Ten-Tails by sealing the Tailed Beasts, who were created from its chakra, into the Statue of Outer Sealing, the Ten-Tail's body. It is revealed that the Ten-Tails was created when Kaguya fused her body into the Shinju, infusing it with her desire to claim all chakra for herself. Fitting for an Eldritch Abomination's stereotypical "huge and hideous" qualities mentioned on the main page, the 10-Tails is so enormous that the 100-meter-tall normal Tailed Beasts are, at best, only one-fifth its size, and it comes in multipleforms that are all distorted and terrifying to look at.
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.
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.
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, 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 Ultimate Madoka, takes her mortal self, then conquers existence and rewrites it to her designs as a paradise for herself and the mortal self of 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.
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 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.