On the left - the Moon. On the right - Hellstar Remina's tongue
The bijuu of Naruto qualify to an extent. Enormous, self-sustaining masses of chakra that take on a form vaguely reminiscent of traditional demons due to the Rikudo Sennin's jutsus, in their natural states they are generally likened to natural disasters. The only real upside with them is they're generally too dumb to use their power effectively. By that merit the 10-Tailed beast they originate from: a creature which seems to endanger the world by merely existing.
The Shukaku, Gyuki, and Kurama all seem to be able to control their abilities to their full effect. Shukaku was able to fight with Gamabunta, a Godzilla-sized Toad without even breaking a sweat after being fully released, and in the desert-unless you have the Fourth Kazekage's Gold Dust it's damn near impossible to stop. Gyuki even before showing it was highly intelligent was a massively strong beast who'd rampage regularly in Kumogakure, killing many shinobi and devastating the village. And Kurama is self-explanatory.
Son Goku, the Yonbi or Four Tailed Monkey is also in complete control of his power. Its also mentioned that all tailed beasts have names given to them by the Rikudo Sennin himself-Shukaku, Son Goku, and Kurama (the Kyubi) are the only ones known. And according to the Hachibi, they have feelings.
Yes, they are powerful. But a skilled jinchuuriki can focus that power and use it intelligently. The three mentioned above just rampaged senselessly without a plan, and so were easier to defeat than if they had an intelligent human mind guiding them. Imagine if Shukaku hadn't just shot bullets at Gamabunta, but had taken the time to convert the area into a desert like Gaara did.
Getter Robo: Another Humongous Mecha work of Go Nagai -and, mainly, Ken Ishikawa- gave us another eldritch abomination. It is inmensely 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 up 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 damaging it slightly. Its name? GetterEmperor, the final evolution of Getter Robo.The narration goes as far as to state: "The voice quakes the universe itself was indeed that of Ryoma Nagare"
Much more Pride: the other homunculi call him a monster. When he isn't masquerading as a little boy, specifically Selim Bradley, his form is that of a mass of shadows filled with eyes and mouths, which often rears up in the form of Combat Tentacles. In other words, he's pretty much a less powerful version of Alucard.
Their creator, Father, even more so. He originally looked like Pride (well, except for the "human young boy" part). He was just a black blob with eyes in a flask labeled "Homunculus". Then he got a copy of Hohenheim's body. Then he turned into a living blob of shadow covered with eyes and mouths that assumes a mostly human form, and in Chapter 104, it goes Up to Eleven: after activating the nationwide transmutation circle and absorbing the souls of everyone in Amestris, Father transforms into an immensely magnified version of his previous, already disturbing form, with added physical characteristics reminiscent of the zombie soldiers that debuted in earlier chapters. He then uses this additional size to rip God from the sky and cross the Bishounen Line to become a Humanoid AbominationPhysical God.
The Gate of Truth, which is basically 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 other's 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.
Digimon Tamers, in which the final enemy was the D-Reaper, 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. Also noteworthy in that it is both man-made and technological in origin, which as noted before is extremely rare.
Guilmon's 'bad' form◊. Hell Guilmon started off as a friendly kaiju (behemoth), but his 'natural' 'Mega' form is such an abomination that its very existence tears apart the digital world (Megidramon is the most powerful Digimon in any of the digital universes).
Apocalymon from Digimon Adventure probably also counts, being 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 also 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 named The Call of Dagomon. Despite the ominous ending of the episode, as well as repeat appearances by the Dark Ocean later in the season, Dagomon himself never showed up again.
Digimon is FILLED with these, such as Chaosmon, Chronomon Destroyer Mode, and Lucemon, among countless others...
Both the Orichalcos stones in the Doma arc of Yu-Gi-Oh! 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 having 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.
And then there are the Earthbound Gods (aka Earthbound Immortals/Jibakushin) from Yu-Gi-Oh 5Ds, the evil entities sealed into the Nazca Lines, and a serious threat to the protagonists (frequently yielding Oh Crap reactions from those about to get creamed). Although a couple look a bit silly (e.g. googly-eyed lizard Ccarayhua — though those eyes would probably give small children nightmares — that and the fact it can eat you if you push its owner too far). And apparently they're all just mooks compared to the King of the Underworld, but they decided that plot point wasn't important.
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.
Raphaello from B't X is a homebrew version of this: Amorphous, constantly growing, Nigh Invulnerable and assimilating everything in its path.
Aizen's Hogyoku-fueled transformations are seriously deformed. This◊ is the final result.
The thing from the third movie, that is an obvious homage to Cthulhu.
Muramasa from the filler saga, who, from Hollow eating like Seigen, turns into this, is also a prime example
Soul Eater's Great Old Ones/Warlords qualify for either 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'.
The same section of the manga basically confirms that Excalibur is one of these as well. Well... he has been known to drive people insane, after all.So he reprsents Rage.
Also, Kishin Asura, before he puts his skin back on, can (sort of) be considered as one of these. Also, Kishin Asura's superpowered, gargantuan form that he gets after he eats Lady Arachne's soul. Fitting, as he IS the aforementionned Warlord of the madness of terror.
In Berserk, the Godhand, many, many Apostles and some Qliphoth creatures count as Eldritch Abominations, being thoroughly unnatural creatures who are all extremely powerful. However, most of the more powerful Apostles seen (Zodd, Grunbeld, Locus, and later Irvine) are not Eldritch Abominations, interestingly. There is also Shiva, the form that Emperor Ganishka took during his final battle with Midland.
The "sea-god" monstrosity from the latest arc is definitely one as well; it even seems to be a deliberate Shout Out to H. P. Lovecraft.
The Idea of Evil, who created and rules over the Godhand. The chapter where it's seen may have been removed due to The Reveal being too early in the manga, but absolutely nothing so far disproves its canonicity.
That being said, they subvert the aspect of a traditional cosmic horror in that, unlike the normally unfeeling monstrosity you expect, as they are intimately connected, and interested to to humanity. Thisisn'tagoodthing. '''AT ALL.
The Angels from Neon Genesis Evangelion are Eldritch Abominations, each one more abstract and bizzare than the last. With one or possibly two exceptions. By extension, this also applies to the Evas and Rei.
But the Angels seen in the original series are mere shadows in comparison to the true abominations, Adam and Lilith. 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.
Their bizarre nature is brought Up to Eleven in the Rebuilds, where they are animated using CG, which makes them appear even more unnatural than usual. Ramiel and Sahaquiel are the most notable of the Angels for this, while Zeruel and Bardiel are more conventionally animated while being no less horrific in nature. Special note goes to Ramiel for the impossible transformations it goes through to utterly destroy the surrounding landscape, which are honestly mind-boggling to watch.
Also the eponymous demon beast from Demon Beast Invasion by the same creator, though it became this late in the series after constant RetCons about a lot of important plot points. It starts out just being a single member of a native Earth species that was driven off millions of years ago by changes in the planet's living conditions who sought to recolonise their old home through rather unpleasantmeans, but ends up a colossal transdimensional monstrosity capable of sending a space station into a space-time void zone. Bonus points for having a cult dedicated to it by that point.
A common Epileptic Tree is that Guu is one of these. She's rather cute and seemingly benign (if mischievous), but the shadowy, formless thing which may or may not be her true form bears a rather Lovecraftian air.
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.
Majin Buu of Dragon Ball Z. 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
Alucard in Hellsing is gradually revealed to be one of these as the series progresses. Sure, he's mostly some variation of humanoid, but then there's the times when parts of him transform into an amorphous void◊ full of demonic eyes and teeth that tend to turn even fellow monsters into gibbering pants-wetting wrecks. This finally culminates in him becoming a tide of blood large enough to drown a city. Turns out all those eyes are the eyes of every person he's ever eaten, including several entire armies.
Do note that "amorphous blob of darkness and eyes" is one description of Samael, the Angel of Death. Alucard is directly compared to Samael on at least one occasion.
Schrodinger is certainly less intimidating but arguably even more eldritch. He exists, as he says "everywhere and nowhere" although only in once place at a time. Shooting him in the head leads to him simply showing up elsewhere an instant later. In one instance he sends a message by simply appearing inside another person's mind. Then Alucard eats Schrodinger.
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. When the whole universeis a cosmic horror, it's not just time to stop exploring. It means all of mankind's victories are merely delaying the inevitable, using up its resources and sacrificing even its best weapons and champions to desperately extend its existence.
Heroman has Vine Monsters in one episode that seem to evoke this trope; as it turns out, the Vines are of Alien origin, and are 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 Baccano!, the "demon" summoned on the Advena Avis, Ronnie Suchiart, is heavily implied to be closer to this than an actual demon. It's also implied that he Was Once a Man.
The Shinigami King from Death Note was never seen in the anime. But a brief flashback in the manga reveals he looks like this◊.
In contrast to a lot of 'abomination' stories where humanity wakes them up, the Novas subvert this by declaring war on us for no other reason than sadism. What they do to the Pandoras just shows they are an entire race of complete monsters.
The Lily Carnation from the sixth One Piece movie, Baron Omatsuri and the Secret Island, is most certainly this, especially in it's true, grotesque form.
In the One Piece 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. What's worse is it hasn't been addressed since and is (so far, knowing Oda) Left Hanging (considering his love of Chekhovs Tropes, however...).
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, setient and capable of resisting its Driver's will. It can destroy most Cybodies effortlessly and those who are already broken can be ressurected 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 from Tengen Toppa Gurren Lagann are this, having godlike powers allowing them to break up laws of physics, create living battle ships as they want, all pretty scary in different ways each, 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, Being capable of creating galaxy-sized Humongous Mecha at an instant, without using Spiral Power and having very creepy forms, similiar to a Living Shadow. Worth noting that They were actually a normal race, that evolved into an ultra-powerful Hive Mind. Though, in a form of general subversion they are actually beings of order, or at least see themselves as such.
They're a unique kind of Eldritch Abomination, in that they made themselves like this. Meaning that they're also physical gods as well. And by Physical God, I mean they're nigh-omnipotent in their pocket universe.
The Anti-Spirals actually consider beings with Spiral Power to be this, with Spiral Energy's ability to end the universe.
The titular mech as well. 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 pretty much a giant robot that doubles as an Energy Being.
The Destroyer from Claymore. 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 also qualifies, as being the strongest damn thing in the Claymoreverse. Clare had to fuse with the Destroyer for any chance of beating her!
The Ghoul from Divergence Eve, bizarre extradimensional maybe-biomechanical space monsters whose presence screws with space-time something fierce.
Rosario + Vampire's take on Alucard is this. He was originally a vampire who achieved so much power that he became a nigh-invincible monstrous being (with aXenomorph head) and went on a rampage that nearly destroyed the human world, if it wasn't for the intervention of another superpowered vampire (Moka's mom).
Tsukune is on the verge of becoming a second Alucard and is already veering dangerously close to Humanoid Abomination territory.
The title being of Gankutsuou, probably one of the creepiest anime abominations out there.
Some of the Dead Apostle Ancestors, such as the Forest of Einnashe, Primate Murder, and Tatari, also fit here, which makes sense, given that vampires in the Nasuverse originate from Brunestud of the Crimson Moon, which is one of the aforementioned Ultimate Ones, although it is rather more human in appearance than the others.
The Gods and Demons from Ah! My Goddess are shown to be this. Though they mostly look like humans (some of them, notably Urd and Peorth are vain and prefer looking like humans), they assume those forms when they come to grant a wish to humans because their true forms are incomprehensible.
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. The scariest part? Magical Girl Lyrical Nanoha As Portable: The Gears Of Destiny revealed that the Book of Darkness was originally created by the Precursors as a seal for an even worse Eldritch Abomination called the Unbreakable Darkness.
Yaiba has Princess Kaguya's true form, which looks like a colossal, black blob with many hydra-bunnyish heads and huge grin. Then there's Yamata no Orochi, who basically is a eigth-headed JAPAN-SIZED dragon that can erase whole countries in a matter of seconds.
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 user, because they resonate with Noise, forcing them to obey the laws of physics.
The new release of 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 basically a writhing mass of alien three fingered hands with biting mouths at their tips http://mangafox.me/manga/hakaijuu/v01/c001/46.html which as the last panel shows may be connected to an even larger creature http://mangafox.me/manga/hakaijuu/v01/c001/68.html. The youtube video reviewing the manga shows that this will only get worsehttp://www.youtube.com/watch?v=3WvvC1awEDA