Retcons to the Transformers backstory turned the planet-eating Unicron into an Eldritch Abomination, not only giving him the power to move between dimensions and universes, but also insinuating that a piece of his dark soul inhabits all of the Transformers since the beginning, meaning that any one of them could turn into a servant to his apocalyptic hunger. Just listen to his theme song.
It was also revealed that he does noteat planets for sustenance - he gets that from hatred and strife. No, he eats planets because he's offended by existence. All of it. So he's trying to eat it. All of it. Every dimension. He's already devoured approximately 20% of all known existence in the multiverse and is eager to continue his binge. He even apparently once destroyed reality itself, and the only reason that anything exists at all is because he missed a couple of fragments and fell asleep, allowing them to rebuild.
In Transformers Prime, Dark Energon is revealed to be Unicron's blood. This is a substance that makes anyone that uses it hear Unicron's thoughts, gives them a serious power boost, almost kills a human (Raf to be exact), and above anything else, resurrects dead Transformers as mindless berserkers. If his blood can do that...
And as of "One Shall Rise" it's got worse. The earth formed around him. And he can make copies of himself in the rock, and keep making them until you're dead. (They're smaller than the original, thankfully, but still huge.)
Dark Energon isn't the only version of Unicron's bloody that did horrifying things; Angolmois is liquid chaos, causing completely random and often puzzling effects. In the comics, it made one into a Herald without them even realizing it, mutating them into monsters that frothed green and granting extreme amounts of power.
The Swarm in Transformers: Generation 2 could also be considered an Eldritch Abomination, being born from a long-lost ritual of Transformer reproduction that their god Primus never intended them to retain, and obsessed with destroying all mechanical life in the known universe. Generation 2 also introduces the Liege Maximo, a massive creature, implied to be one of the original Primes, who's something of a Unicron Expy, but nonetheless an Abomination in his own right.
The original series episode "Dweller in the Depths" takes some obvious inspiration from Lovercraft. Tornedron from "Call of the Primitives" could also probably count as an artificial abomination, and it is rather anticlimactically beaten by flicking a switch, reversing its polarity.
In the pilot episode, something called "Imperium" appeared, a big night-loving blob with tentacles.
One of these bought the galaxy in an eBay auction during a Futurama episode: "SOLD! To the being of unspeakable horror!".
Another one attempts to date and have sex with the entire universe in the second movie.
"So, Elzar, what are you preparing for Morbo to devour with his mighty jaws?" "Morbo, I'm whipping up a nice unnameable horror from beyond. With mango chutney!" It's not made clear how good it will actually taste, but it appears to emit truly terrifying amounts of some sort of radiation. Probably very hygienic.
Teenage Mutant Ninja Turtles (2003) featured one of these in the episode "The Darkness Within", who arrived centuries ago in the form of a meteor and sucks the life energy of its victims as they visualize their worst nightmares. However, its most heinous feat may have been its subconscious influence on the greedy, which caused them to gravitate to Manhattan, and was therefore indirectly responsible for the existence of Wall Street.
The Nergals also have obvious traits of this, especially Junior; in addition to shapeshifting, he can walk through walls, freeze people in stasis and spawn bat-like imps from his own body. His true form is so hideous that they didn't even show it onscreen until it (ostensibly) appeared in "The Greatest Love Story Ever Told Ever".
The Santa suit from Invader Zim is a colossal, indestructible, self-aware mechanical beast that, millions of years in the future, waits in space to gather energy until it is strong enough to return every year on Christmas to eat. The only cities (or maybe the only city) to survive do so under a powerful energy shield. Fortunately, it's appetite can be sated with milk and cookies.
The Infinite Energy Absorbing Blob as well, considering that its name is very much appropriate, and it was so powerful that even the mighty Irkens could do nothing as it rampaged through a high-tech facility and ate their highest leader. (Twice.) Zim created both of these, but he never intended for them to be so uncontrollable.
Superman the Animated Series had as a one-time threat a Hive Mind alien blob thing that called itself "Unity". Using a creepy preacher as its primary avatar it turned Smallville into a Town with a Dark Secret that nearly absorbed all the townsfolk into itself.
The episode featuring Dr. Fate includes a Cthulhu-esque villain tries to take over the world and turns all of Superman's friends into misshapen elder things.
In Chaotic, the M'arrillian Tribe is hostile sea food at the lower-rungs, but at higher rungs, like Chieftains and Aa'une himself, are mostly eyes and slimy tentacles that don't look like anything. Aa'une's One-Winged Angel form with multiple mouths and a dozen tentacles now makes him by far the ugliest creature in the entire series.
The Greedy from Raggedy Ann And Andy A Musical Adventure.
Super Robot Monkey Team Hyperforce Go! has several of them, like a flying multiple-eyed thing that turned anybody who looked at it into bloodthirsty zombie among many others. And Skeleton King's master was a fricking big earthworm-like thing that was much larger than anything else our heroes ever meet. And It was only a part of its original body, God knows how big.
The eye monster was Skeleton King's eyeball. Wow... If each body part of him is an Eldritch Abomination, then what does that make him?
Also, an episode late in the final season has a flying minotaur-like thing with the ability to open a portal to a dimension filled with fellow Abominations. And during the finale, the team actually travels to that dimension in pursuit of Mandarin, Valeena and Evil!Sparx, thus exposing the audience to even more Nightmare Fuel.
There's at least one in Metalocalypse; thing is, we don't know whether it's someone in the band, the whole band, or Selatcia... Or all of the above.
Avatar: The Last Airbender has Koh, a malevolent spirit resembling a giant centipede. Despite his affable behavior, he is widely feared for his hobby of stealing people's faces. And if a visitor shows the slightest hint of emotion, Koh adds their face to his collection. Kind of a One-Scene Wonder character, but still.
There was an old episode of G.I. Joe where it was revealed that a bunch of furry cultists living in the ruins of Destro's family castle worshipped a "thing" that dwelled in the deepest pits of the place; we don't see much of it except for a cycloptic eye and some reddish tentacles.
Lucubra, the main antagonist of the Ben 10: Ultimate Alien episode "The Creature From Beyond" and possible Big Bad of the season if Paradox's warnings are any indication. This extradimensional horror boasts Super Strength, Nigh Invulnerability, Frickin' Laser Beams, and the power to devour a person's thoughts with Mind Control as a bonus...and that might just be the tip of the iceberg.
All supernatural characters on the show are either connected to aliens (i.e, the Omnitix and Ultimatrix), magical phenomena (Like Hex and Charmcaster) or both (Gwen in the main timeline). This creature appears to be none of the above.
Vilgax's One-Winged Angel form actually gets mistaken for Dagon by a cult. While they believe Dagon to be an alien, their cult-like mentality and beliefs are more like worship. Rather this is meant to be a shout-out to the actual pagan god or the Great Old One is unknown but how they treat him has an Eldritch Abomination feel.
The real Dagon. It's held behind the same seal as Lucubra, but is much worse (Gwen says compared to Dagon, Lucubra is an insect!). In the next episode, they're actually shown the Diagon, and while the audience doesn't see it (though commercials very clearly show him) Gwen and Kevin react to seeing him as if they were in pain.
The Lub Glubs, essentially shoggoths from the Cthulhu Mythos who wear jolly inflatable pool toys as skins. When attacking, they shed the pool toys and reveal their true forms: inky black blobs covered with toothy mouths.
The Ancient Ones from Hot Wheels Battle Force 5, beings heavily implied to be the Big Bads of season 3, are shaping up to be this. They're an ancient evil that predates the Sentients (who created the multiverse), whose mere awakening begins to spread darkness throughout the multiverse. Rawkus, a being whose purpose for existing is to maintain Balance Between Good and Evil, considers them evil enough to be firmly on the side of the Battle Force 5 against them. What we've seen of their appearance, shadowy figures during Rawkus' monolog about them, is even more disconcerting.
The Windigos, shown in "Hearth's Warming Eve". Spirit horses that feed on hatred to bring eternal winter, they're even based an awful lot off the version of the Wendigo from the Cthulhu Mythos, who was an Eldritch Abomination as well.
The demon that Mok wants to summon in the movie Rock and Rule is definitely in line with this trope, with its lack of a fully defined, stable form, immense power, and its actions being more akin to an all-consuming supernatural force of destruction than those of a recognisably sentient being.
