Hunson Abadeer, an unkillable, hideous monstrosity who rules the Nightosphere in a perpetual state of chaos and pain, has a One-Winged Angel form Lovecraft would have been proud of, and whose first order of business when he managed to escape was to suck up the souls of everyone in Ooo. How Marceline ever managed to become a Chaotic NeutralCute Monster Girl with that as a parent is a riddle for the ages.
Abadeer's amulet, made of "pure chaotic evil", turns the wearer into an Eldritch Abomination within seconds. This happens to both Marceline and Finn.
Heck, any of the Spirits encountered in the Avatar-verse in whatever medium covering it are rule-breakers and knee-shakers, whatever form they care to take and regardless of how friendly or unfriendly they are at any given point. No exceptions. Even the Avatar state is not without its scarily worrying aspects. Koh... really manages to pile the creep on with a trowel, though. His mother is no different: it must run in the family.
Vilgax's One-Winged Angel form gets mistaken for Diagon by a cult. While they believe Dagon to be an alien, their cult-like mentality and beliefs are more like worship. Rather, if 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 Diagon. It's held behind the same seal as Lucubra, but is much worse (Gwen says compared to Diagon, 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. Just take a look. He comes from another dimension, is referred to as an 'Old One' by Charmcaster, and has enough power to match and defeat a powered up Way Big (one of Ben's most powerful aliens, if not THE most powerful).
Chernabog from Fantasia is an obviously Sataneque being who is shrouded in darkness and having entire mountain as his lower torso. He is able to raise the dead, manipulate flames and change things into twisted parodies of life.
Courage the Cowardly Dog dealt with these things all the time. Most notable was the blue... well, whatever you want to call it from "Perfect." Despite only having about 10 seconds of screen time, it was one of the scariest and most notorious creatures in a series known for having scary things.
An easter egg in the Gravity Falls episode "Irrational Treasure" lists on the top-secret Northwest Cover-Up document that there is an enormous, evil, time-devouring baby from another dimension that is frozen in an Antarctic glacier. "The Time Traveler's Pig" reveals that the "Time Baby," as its mortal supplicants dub it, is eventually released and conquers the world... or at least establishes the Time Police.
The Grim Adventures of Billy & Mandy: The Nergals, 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". Note that Junior isn't always evil. (If you don't make him angry, he can be somewhat decent.)
The Greedy is a shapeshifting mass of sentient taffy lacking the ability to stay in a shape for longer than a few seconds, while eating candy that it constantly regurgitates.
Short-lived (only 13 episodes long) 80's Hasbro series Inhumanoids revolved around the heroic "Earth Corps" fighting against ancient, kaiju-like horrors from the center of the Earth. The three main antagonists were Metlar (giant mineral-based demon who throws globs of molten rock/iron at his foes), D'Compose (rotting zombie dinosaur who could revive the dead and turn the living into decaying zombie slaves with a touch) and Tendril (Cthulhu-like plant-monster). Others appeared in several episodes, like Gagoyle and Ssslither, whilst recurring foe Nightcrawler was a Humanoid Abomination created by D'Compose from the corpse of a human enemy.
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 recognizably sentient being.
In the backstory of Samurai Jack, the gods hunted and defeated an Eldritch Abomination, but missed a single fragment. That fragment fell to Earth and eventually became Aku.
In "Coon 2: Hindsight" and "Mysterion Rises", DP (formerly BP) drill into another dimension and release Cthulhu.
Cartman becomes one in "Trapper Keeper" when he is assimilated.
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 zombies, 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 his 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.
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.
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, causes feelings of intense nausea and illness upon first contact (though eventually it is possible to build up a resistance), almost kills a human (Raf, to be exact), and, above anything else, resurrects dead Transformers as mindless berserkers, allowing living ones with enough Dark Energon to control them unless Dark Energon is mixed with something such as synthetic energon. 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.) Later on, it's revealed that it can revive lobotomised consciences, and that mixing it with artificial compounds such as synthetic energon causes mutated Terrorcons to be created, essentially vampires in Transformer form, as several poor Vehicons, all the Insecticons, Airachnid and Silas / Cylas found out.
Dark Energon isn't the only version of Unicron's blood that did horrifying things; Angolmois (from Beast Wars II. Dark Energon is basically Angolmois by another name, though the makers of Transformers: War for Cybertron say it's pure coincidence) is liquid chaos, causing completely random and often puzzling effects. In the comics, it made someone 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 was born from a long-lost ritual of Transformer reproduction that their god Primus never intended them to retain, and is obsessed with destroying all mechanical life in the known universe.
Also, the big reveal of Transformers Armada is that the Mini-cons are created from Unicron's cells. Keep in mind how powerful they are, especially when brought together. Earth-Shattering Kaboom power in the right combination, and this magic, pretty 'song' they do. It's all part of him.
In Sabrina: The Animated Series when Sabrina, Harvey and Salem are trapped inside Harvey's comic book world. They encounter an entity known as the Dreaded Dysphilia. It appears as a flying blob of fungus that erases everything in its path forever. What's more is that Harvey's negative self-esteem makes it bigger. That's right - a monster that is powered by the negative self-esteem of a teenager. What's more is that it's completely alien to the comic book world - Harvey didn't even create it.
The infamous Paraphernalia Wagon from Halloween Is Grinch Night releases a truly bizarre assortment of creatures, referred to as the "Unhuman Race."
In the Superman: The Animated Series episode "Warrior Queen", the traitorous suitor De'Cine dumps Maxima, along with Superman and his own partner Sazu into an abandoned sewer system where a thing called the Carnorite lurks, a gigantic, tentacled monstrosity that is so big, its tentacles reach throughout the whole sewer and you cannot see the whole creature in one glance. (When Superman asks Maxima how big it is, she simply says, "Big!") He's able to defeat it by tricking it into grabbing an electrical generator with its huge tongue, but that likely only managed to stun it long enough for them to flee.)