The Cjopaze from Ruby Quest is apparently the force responsible for downfall and corruption of the facility and also the reason why the Brig/reality has been tearing apart over the course of the story.
Homestuck features the Horrorterrors, monstrous beings which live beyond the outer rim of the microcosm of a game of Sburb. The only one known to exist outside of the game is capable of killing off all intelligent life in the galaxy with a single (probably psychic) sound. Oh, and there's a distinct possibility that they're among the good guys in the greater scheme of things.
You know the Squiddles? The ridiculously adorable plushies that Taste Like Diabetes? Yeah, turns out that they're humanity's subconscious manifestation of the Horrorterrors.
Lord English could also probably count, seeing as he's an immortal, dimension-hopping demon destined to consume the dead fragments of the universe. He does wear a pretty snazzy coat though.
Much like the Noble Circle of Horrorterrors above, the Dark Lord Inglip is one of the rare examples of a friendly Abomination...well, sortof.
Humorously addressed in an advertisement for Elder Sign.
The SCP Foundation deals with these things on a regular basis.
SCP-058, a gigantic bovine heart with insect-like legs and tentacles that constantly speaks cryptic nonsense in a monotone voice, and SCP-682, an extradimensional, shapeshifting reptilian creature with a murderous digust of all life. SCP-682 can also regenerate from everything this includes vaporisation, being cut in half, getting shot into the sun. oh and SP-343 who is basically god said that "he isnt one of mine, deal with him yourself, yeah. It also has a disturbing tendency to make any shapshifting, transmuting, or creation capable SCP to make another copy of him to the point of being a Running Gag
Whatever was responsible for the destruction of the world accessible through SCP-093.
SCP-1129 gives the imperssion of being an Eldritch Abomination. That is, anyone viewing it directly, or viewing a photo or video of it, immediately becomes convinced that it's intrinsically wrong, should not exist, and must be destroyed. However, looking at an illustration of it merely gives the impression that it's strange. Technically it shouldn't be able to exist in our universe, since it seems to occupy more than the usual three spatial dimensions, but that shouldn't cause people to react to it with hatred, loathing and fear.
The "Jackal" in another called "The Cave" certainly is. Carvings of it found in the cave are all mostly scratched out. When the protagonist sees it, it's so incomprehensible it really looks rather like that.
The PodcastCritical Hit's main antagonists are The Void, a group of insane Gods who inhabit the world's moon. They are all insane, powerful beyond belief and have wonderful names such as "She Who Slumbers In Agony."
The Protectors of the Plot Continuum have gone up against a version of Nineteen Eighty-Four's Big Brother - or at least something that identified itself as such - in the past, despite it being contrary to Big Brother's canonical treatment. The Mary Sues also count, though they're invariably incredibly beautiful humanoids, and there's been at least one instance where excessively Purple Prose created a sentient purple cloud which proceeded to take over the Word World and antagonise the agents; it went away as soon as the Author-wraith was dealt with, however.
Something Awful and /co/'sDogscape, a colossal organic mass of dog parts smothering the entire globe leaving only trees growing puppy fetuses and occasional masses of milk teats as the only sustenance for the few remaining scraps of humanity.
Most of the holders are eldritch abominations, or have one nearby. Most of the stories include one somewhere.
The Transapients, and especially the Archailects of Orion's Arm. The very least of them is as far beyond a baseline human as that human is beyond a non-provolved animal. They are so advanced that their individual thoughts are sentient. Their physical forms vary from "Moon Brains" to entire pocket universes with just a small piece sticking out into reality.
And most of those listed are "friendly" to humanity, there are also entities that turn entire colonies into masses of flesh and metal as "art".
In Fine Structure, the Big Bad is an Omnicidal Maniac type, and there's another one ("The Imprisoning God") keeping him somewhat in check. technically the Big Good is one as well, but he spends most of the story as a human being.
In There Will Be Brawl, we get the multiple Mr. Game And Watches once they use their Final Smash. This is especially surprising because they are seen all over the city earlier, socializing and holding down normal jobs.
Little Lenny Penguin and the Great Red Flood is chock full of these. Most are antagonists, but the occasional friendly eldritch protagonist comes along and helps Lenny and the gang (Wrigley, Quack, partially Half-Face). They reside in a hellish Dark World where the vast majority of the story takes place.
Todd: Part of me resents the idea that she's the pop star that it's safe to like. And I don't mean safe, in that she's less likely to devour you.
During his encounter with the Makeover Fairy, the Fairy saw what was under Todd's mask which, given her reaction, seems to be based on non-Euclidian Geometry.
Lambda features the beast called "Ichi". It is said to guard a power source called the White Pool.
"Its horrifying appearance cannot be fathomed by a thousand wise men. They would go mad before seeing its partiality. Its unrecognizably twisted mind – if that is indeed what it is – cannot be predicted by a thousand prophets. They would perish before probing its shallowest depths. Its power cannot be harnessed by a thousand magi. They would melt and explode from its uncontrollable flow."
From the recent Web Game Reimagine :the game:, The Boss definitely qualifies.
This is what The Fear Mythos is all about. There are a few Humanoid Abominations (The Slender Man, the Cold Boy, the Blind Man) and then there are the Starfish Abominations like EAT (sentient water that can replace all the water in your body and take you over) and the Empty City, which traps its victims inside itself, making them wander around its evershifting structures until they die.
