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. According to the comics he became ruler of the Nightosphere by deposing some even nastier abominations.
Prismo is a being of unlimited power who lives outside of time and space at the centre of The Multiverse, casually creates (and destroys) entire Alternate Universes, and doesn't even have a physical form so much as he's a projection of the Time Room, but fortunately he's a pretty friendly guy. In the Wham Episode "Wake Up" Prismo's true form is revealed to be a sleeping old man who manifests whatever he dreams about in the real world.
Bella Noche is "a being of pure Anti-Magic" from another dimension. It first appears as a slimy green head, and upon entering our dimension it is a giant black cube that constantly expands and neutralizes the magic in anything it comes into contact with. Attempts to stop the expanding cube only caused it to expand and mutate further. Doesn't stop Betty from defeating it by punching it in the face.
The interdimensional beast "Jojo" in "Mandarker". He apparently helped Mandark write the book The Magic of Science by Mandark and Jojo, but when Mandark summons him as part of a science fair project, he goes berserk and tries to eat Dee Dee.
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).
In the comics, Ian Karkull is a guy with shadow powers, but in this, it's like the writers didn't know if they wanted Cthulhu or Satan and so combined them. A common hood gets his hand on a tablet and reads it aloud. Bad idea. He becomes the host to a shadowy tentacled something that wants to create Hell on Earth and basically overwrites the Daily Planet with his own unreality, everyone caught within, Lois and Jimmy included, becoming possessed and transformed by the demonic creatures that live there. There's a seemingly bottomless pit in the center. In the end, Superman has to chase the dropped tablet (Doctor Fate needs the original tablet to undo it all) down this pit, and it turns that if you go far enough, farther than the eye can see from the surface, the pit does have a bottom. The bottom has a mouth. The bottom is also rising.
An easter egg in the 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.)
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 Rock and Rule lacks a fully defined, stable form, has immense power, and its actions are more akin to an all-consuming supernatural force of destruction than those of a recognizably sentient being.
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, and 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.
In the backstory of Samurai Jack, the gods, Odin, Vishnu and Ra, hunted and defeated Evil itself, a black mass of pure nothing. A single fragment survived and fell to Earth and eventually becoming 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.
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. His first appearance in Transformers: The Movie shows how abominable he is when he devours a throwaway planet in all its gruesome detail in a way that reeks of a Cosmic Horror Story. Shots of his bizarre pseudo-biological inner workings make his strangeness even more pronounced.
He does noteat planets for sustenance - he gets that from hatred and strife, and will exist so long as these things do. 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. When he's done, space itself as we know it will be eaten. He 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, 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 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...
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.
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.
An episode of The Wild Thornberrys set in Africa had Eliza and Darwin venture into a forbidden patch of the jungle where a demon, monster, or something even worse supposedly dwelled. The seemingly supernatural events that occur throughout the episode could be regarded as Eliza simply hallucinating from panic and fear... until the very end.