The Godhand, many, many Apostles, and some Qliphoth creatures, being thoroughly unnatural creatures who are all extremely powerful. Interestingly, most of the more powerful Apostles seen (Zodd, Grunbeld, Locus, and later Irvine) are not Eldritch Abominations.
Shiva, the form that Emperor Ganishka took during his final battle with Midland.
The Idea of Evil, who created and rules over the Godhand. That being said, they subvert the aspect of a traditional cosmic horror in that, unlike the normally unfeeling monstrosity you expect, they are intimately connected to and interested with humanity. Thisisn't agood thing.
After fusing with the Hogyoku, Sosuke Aizen goes through several weird-looking transformations, but the one that fits best is the fourth. After spending his life as a Shinigami, the Hogyoku deforms Aizen into a grotesque Hollow-like creature with a distinctly humanoid structure◊. A Shinigami has a Zanpakuto, while a Hollow has a mask. Aizen turns into a being that boasts neither, with his arm becoming a blade and his face splitting open to reveal his skull.
One of the games introduces Seigen Suzunami. Like Aizen, he's another Shinigami, but Suzunami is notable in that he eats a Hollow known as a Gillian (towering skyscrapers with cloaked, elongated bodies and a massive face-like mask that sport a spiked nose). It turns Suzunami a giant of a man◊, with pale white skin, glowing red eyes, a long red mane, Hollow mask remnants covering the upper right side of his face, and a partially opened Hollow hole in the center of his chest. He follows the "Eldritch" part after eating three more Gillians, deforming himself into a large serpent-like creature with black tentacles, and a large mirror placed in the center of his body◊.
"The Invisible Thing" sealed inside Touma, which is released if his right hand is ever cut off. Whatever it is, it is so powerful that a guy claiming to be more powerful than God was terrified of it, and nobody in the world seems to have any understanding of what it is, except maybe Aleister Crowley, and he's not telling.
DRAGON, aka Aiwass. It looks sort of like an angel, but it sure doesn't act like one, nor talk like one. All that is known is that it is an infinitely powerful, immortal, and incorporeal existence. It has only been attacked once, by Accelerator, and it stomped him flat in no time with its unconscious defenses. Even Accelerator admits that he has no idea exactly what it did to him when it attacked.
A Certain Scientific Railgun: The fetus-monster at the end of the Level-Upper arc, actually a huge AIM disturbance caused by the 10000-Esper-strong Level-Upper network going haywire. Shoot it with Misaka's up-'til-now-foolproof railgun? It just keeps getting bigger. It's enough to merit an Oh Crap from Misaka.
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 observing Priscilla came to realization 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 Descendants of Dragons that are allied with the Organization's enemy are truly bizarre and majestic monsters whose flesh is the source of the yoma and by extension the Claymores. They live for up to 200 years without visibly aging, are hermaphrodites, and start out as Gigeresque humanoids twice as tall as any human with the ability to permanently "Awaken" into mighty beasts. And unlike the Claymores and the yoma, they were never human at all.
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.
Guilmon's first Mega form, Megidramon◊. Guilmon started off as a friendly kaiju, but his 'natural' 'Mega' form is such an abomination that its very existence tears apart both the digital and real worlds. (Megidramon is one of the most powerful Digimon in any of the digital universes).
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 it, causing its time to flow at a different rate to the Real World and also causing the creation of powerful evil Digimon.
The Digimon Adventure 02 episode where Kari gets taken by weird fishlike Digimon to the Dark Ocean is a rather obvious reference to the Mythos. They want to give Kari over to their master, Dagomon (who, despite being seen only as a shadowy form, is eerily similar to Cthulhu), and when she refuses, those fish Digimon change into shadowy... things that may not be Digimon at all. Well, the episode just happens to be named The Call of Dagomon.
Others include as Chaosmon, Chronomon Destroyer Mode, and Lucemon.
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.
Arkadimon from Digimon V-Tamer 01. It can't talk, only making creepy sounds, is far more powerful thananything of its own level, and evolves much more quickly than it should by absorbing all of other Digimon's data.
Millenniumon takes the Digimon cake. It started out as a fairly standard, if super powerful, fusion of two ordinary digimon, but quickly transformed into some bizarre Energy Being Dragon thing that is pulsating out of a rift with a few rows of data keeping its power in check. It was so enormously powerful that the entire digimon multiverse (that includes all the seasons, games, and manga) was about to be conquered or destroyed, depending. The only way they beat it was it willingly choosing to trap itself by fusing with a weaker digimon.
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.
Janemba, a demon that was created by the pure evil energy of all the souls who have gone to hell from the last thousand years. He transforms from a Chaotic Neutral childish Reality Warper to a Chaotic EvilOmnicidal Maniac, similar to kid Buu but in a big red devil form. His power is so great he was able to transform hell into a sugar bowl.
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 is 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, but 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.
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.
Gluttony is even worse in the movie for the 2003 anime: it's a gigantic pale white....THING.
The title being of Gankutsuou, probably one of the creepiest anime abominations out there.
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 of its can blow to cosmic dust a planet and its fist can crush tears in the fabric of time-space. Vast armies 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 the least menacing ones. And thereare creatures like this.
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; Kuyo Suo is so profoundly inhuman that normal people simply will not acknowledge her existence unless forced to.
Alucard, a vampire who assimilates the souls of his victims by drinking their blood and is able to summon them at anytime. Being 500 years old, he is able to summon millions. He is also able transform into some sort of... thing that looks like a mix of shadows and blood filled with thousands of red eyes.
Alexander Anderson becomes one to kill Alucard.
The Captain of Millenium, Alucard's equal and an example of Primal Fear.
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.
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.
The Tailed Beasts. Enormous, self-sustaining masses of chakra that take on a form vaguely reminiscent of traditional Japanese demons who were created when the Sage of the Six Paths split the ridiculously powerful 10-Tailed Beast into 9 different entities, whose rampages are generally likened to natural disasters. However the Beasts' tendency to rampage is not so much because of any lack of intelligence, but because of their deep-seated resentment towards humans treating them as merely tools; the only Tailed Beast who seems to be truly off its rocker is Shukaku.
Orochimaru's true form is a big demonic snake made up of smaller snakes. Even his pale, snake-like human form is basically this; he can shed his old body like a snake, his blood is a poisonous vapor that can paralyze anyone who breaths it in, and he can take over your body for his own uses.
The Rebuild films turned Ramiel and Sahaquiel into this. The former is living geometry that goes through multiple impossible transformations that are mind-boggling to watch, while the latter is a gargantuan thing with several bizarre forms, and both of them scream when they attack.
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 surpassed everything else seen in the series combined, and even screwed with our real-life psyches. By extension, this makes Kaworu and ReiHumanoid Abominations.
The Lily Carnation from the sixth movie, Baron Omatsuri and the Secret Island, especially in its true, grotesque form.
In the manga, it is heavily implied at the end of the Thriller Bark arc that one of these still resides in the Florian Triangle. Beforehand, we learned that ships kept disappearing when they entered it. Later, we learned Gekko Moriah set up shop there, and it seems like that was it, but at the end of the Arc, a massive figure emerges from the mist.
Pokémon: Toned down some from the games' Pokédex descriptions, but some of the Pokémon remain delightfully creepy.
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.
Kriemhild Gretchen is explicitly the most powerful witch ever, formed from the Magical Girl that one-shotted Walpurgisnacht, and it's mere birth provided enough energy for the Incubator to satisfy its quota for the entire planet. A gargantuan tower of shadow that reaches far into the sky, it seeks to absorb all of humanity into its barrier.
Kyubey (aka Incubator), an amoral enigmatic alien with a Hive Mind, whose composition or psychology we have any little idea of, but utilizes and consumes the mutated magical girls for energy.
Alucard from Rosario + Vampire. His body and blood acts as The Corruption to anyone unfortunate to get infected from it. His body... the best comparison is a Queen Xenomorph, with several tentacles and towering over skyscrapers. His power is so great it took all three Dark Lords just to put him to sleep, and it took Akasha Bloodriver sacrificing herself to seal him again despite her own insane power. And because of his human clone Miyabi and Gyokuro Shuzen, he's back and even stronger!
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 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 soild 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.
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.
In the actual card game, the strongest "Alien" monster is called "Cosmic Horror Gangi'el" and is an alien cyborg with a huge mass of tentacles. The "Alien" theme centers on "infecting" opponents with alien DNA ("A-Counters") that weaken and eventually kill them.
Pegasus' Relinquished and Thousand-Eyes Restrict also qualify.