The Entity from Atop the Fourth Wall. For such a campy, silly show about a Man Child who reads comic books, this thing is terrifying. For one thing, it seems to lack physical form. And from there, it all goes downhill. It's so deadly, the guy fighting it became a Multiversal Conqueror feared throughout creation just to stop it.
The "Jackal" in a Creepy Pasta called "The Cave". Carvings of it found in the cave are all mostly scratched out. When the protagonist sees it, it's so incomprehensible that 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."
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 the Global Guardians PBEM Universe, Lovecraft was right, sort of; he just got the details wrong. The Great Old Ones that invaded this reality at the beginning of time were imprisoned by the Powers That Be (or at least the Powers That Were at the Time), and in the modern day, the heroes have to deal with their remnants, their cultists, and their attempts to re-invade reality.
The Cthonians, the mortal descendants of the Great Old Ones, want to free their ancestors from their mystic prisons. The heroes naturally think this is a bad idea.
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 Rainbow Dash Presents: Haunting Nightmare, we have Smarty Pants, who possesses Twilight Sparkle and plans to be eaten by an even larger eldritch abomination so it can continue it's unholy life cycle. It only fails to do so because Thrackerzod has already laid claim to Twilight itself.
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, though there are also entities that turn entire colonies into masses of flesh and metal as "art".
And then there's the Leviathan, a mysterious and really freaking hugenote approximate mass: 100 billion suns, approximate size: 10 light-years across object that has made contact with the Triangulum Galaxy, and is probably heading to the Milky Way next. Who built it? Unknown. What are its intentions? Unknown. How was it built? Unknown. What even is it? Unknown. Even the Archailects are confused by this thing's existence.
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.
SCP-682 is an extradimensional, shapeshifting, reptilian creature with a murderous hatreds toward all life. It can regenerate from anything, including (but not limited to) vaporization, vivisection, being eaten alive, and being shot into the sun. It has a disturbing tendency to cause any SCP with shapeshifting, transmuting, or creation capabilities to produce another copy of itself (to the point of being a Running Gag). Oh, and SCP-343 (who is God) said, "he isn't one of mine; deal with him yourself". Yeah.
SCP-738 appears to be the Devil in his deal-making guise. It says that the price for elimination of SCP-682 without harm to the world is beyond the ability of the the Foundation to pay. Some time later, they locked it inside a chamber where physics are essentially in sandbox mode, and fiddled with the controls in a way that'd completely annihilate regular matter. The damn lizard enjoyed this.
At one point, they locked it in a story (It Makes Sense in Context) with a benevolent monster who was created by another SCP specifically to kill 682. 682 killed it anyway.
It's much worse than that: the creature wasn't just made to kill 682, it's sole attribute was that it would kill 682 if it ever got near it. And 682 killed it.
Whatever was responsible for the destruction of the world accessible through SCP-093. It granted this world advanced technology, along with "his tears", some sort of purifying liquid that was liberally used to cleanse bodies for anything. Cold? Get submerged in tears. Murderous insanity? Submerged in tears. Cheated on your husband? Submerged in tears. They eventually warped victims into faceless, rampaging zombies that absorbed their victims to become stronger and bigger. The away team encounters several the size of skyscrapers. It gets worse than this. Much, much worse.
SCP-1129 gives the impression 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.
It's implied that SCP-993, aka Bobble the Clown, is one of these and has been alternately hindering and helping humanity. Bobble is just its most recent form.
Most recently they attempted to drain the blood pool. It responded to this by Mind Raping everyone present. The above mentioned time when it went for a long period without spawning any monsters occurred before a different incident when it apparently took control of the minds of everyone stationed at it. It gets worse, several of the monsters that emerged from it were dangerous enough that they had to resort to getting help from another SCP to stop them. One time they sent a submarine into the pool and it emerged into a bizarre alternate world where at least one other known SCP may have originated from, but the thing is, nobody remembers that this event ever happened or that the people involved ever existed. The only evidence that this happened is a single document found in the database. Fridge Horror: it can erase people from existence.Worst of all, they recently noticed that the fluid of the pool has slowly been rising.
SCP-435 is a meteor with one of these bound to it. It's got a very strange shape which includes fractal tentaclesand can only be distinguished with computer enhanced images, is seemingly immaterial, any solids that pass through it tend to get violently accelerated at best, and if the meteor isn't illuminated at all times, the thing can move and grow, and might end up going into the ground, with undesirable results. The worst part? That's just the thing's shadow on this universe, it was he who made the darkness, and hates the light with a passion, which lead to its sealing to the meteor, from which it would take a mere 90 seconds of darkness to escape. Oh, and the emergency plan consisting of "dump the rock in another universe and hope for the best" might just break the seal completely.
He-Who-Made-Dark and his rival He-Who-Made-Light (who apparently isn't any better than He-Who-Made-Dark) appear in several other SCPs. These include SCP-286, SCP-319, SCP-719, SCP-1736, and SCP-1806. Several of there are confirmed by the author to have been created out of fragments of the very same meteor that is SCP-435 and all of them have very disturbing effects. 286 is a game board where the players become possessed by said entities, and the results of the game apparently trigger disasters such as solar flares or the movement of SCP-435-1. 319 is a portal to another universe that will cause this universe to be completely rewritten (effectively destroying it) because of the differences in the properties of the universe it connects to. 719 is a radioactive television through which He-Who-Made-Light communicates disturbing messages and it is implied that he could escape into our universe through it. 1736 is a Bizarre religion based off of 719 whose leader is similarly radioactive. 1806 completely rewrites the way that people perceive reality, allowing them to see entities that exist in shadows and eventually causing them to only be able to speak in Word Salad Horror because our language doesn't have the ability to describe what they see.
The Church of the Broken God worships an entity that seems like a mechanical version of this trope, several SCP objects are believed by them to be pieces of their god. These include SCP-882, a mass of gears that assimilates any metal it touches and Mind Rapes people into feeding it more, SCP-217, a virus that turns living things into machines, and SCP-271 a coin that produces bizarre symbols around it that turn objects into metal, and a few others. The Foundation really does not want to find out what will happen if these objects were to meet, as it potentially could assimilate the whole earth.
SCP-582, nicknamed Bundle, is an extremely dangerous and powerful Slender-Man like creature with many forms and many names. What is interesting is that it is actually a meme that manifests in the real world whenever somebody who has been exposed to the meme writes a fictional narrative about it. If somebody were to write about it destroying the world, it would do so and it would be impossible to stop, except by preventing the writer from finishing the story.
SCP-1739 is a computer containing a program that has the ability to send people back in time, creating an alternate timeline and allowing communication with the alternate timeline, for a period of 3 hours. Whenever it is used an animation of a dog chasing after a ball and breaking it plays. After using the computer several times it was realized that the animation is actually a symbol representing an Eldritch Abomination (the dog) annihilating the alternate universes (the balls) created by the computer, whose purpose is to keep the thing satisfied, so that it won't decide to break out of its metaphorical chain.
SCP-2317 is a doorway leading to a world where an eldritch abomination related to the above mentioned 231-7 is imprisoned and is on the verge of escaping, and it is only held back by regularly preforming a ritual and if that fails then they are prepared to attempt to stop it with a nuke. Most of this information is a lie. It has nothing to do with 231-7, the ritual doesn't actually do anything, and using a nuke will not work. It is all a cover up to keep anybody from finding out that it will escape and there is nothing the foundation can do at this point to stop it.
SCP-2440 is an entity called Xiolt-la whose power increases with the number of people who are aware of its existence, and those who are aware of its existence are compelled to spread this information. The foundation must keep the total number of people who are aware of it at less than 200.
SCP-1055 is also a perception based abomination like the above 2950 and 2440 although it may be closer to a Animalistic Abomination than an Eldritch Abomination.
SCP-1959 is a lost cosmonaut stuck in orbit around the earth while fighting against an unseen enemy. According to this story it is another Eldritch Abomination and he is keeping it from reaching the earth with nothing but Heroic Willpower.
SCP-2001 causes people to believe that outer space is filled with eldritch abominations and that space itself is trying to warn us not to go into space because of the horrors out there.
SCP-1710-1 formerly was an eldritch abomination. It came to our world chasing after another abomination (possibly SCP-682), but found that it couldn't survive in our world and so it sought out a method of reincarnating into a form that could. Unfortunately, it accomplished this by making a deal with atrickstergod, and ended up reincarnated as a tree.
According to this Thread, which is a place for Word of God to reveal secrets about SC Ps not found in their article (which may spoil a lot of them, take warning), the following SC Ps either are or were caused by Eldritch Abominations:
SCP-1382 This is the result of an encounter with one.
SCP-1606 It is caused by a being that is basically a personification of memory loss that is trying to break into our world and currently is possessing the old man.
SCP-1175 It is a creature, and the guard drones it created to protect itself, that got stuck in our world which is unpleasant to it because of it's Alien Geometries being confined by our world and it wants to go home. It is drilling into the ground to gather thermal energy to escape. It eats the people that its guards kill to hide the evidence, not out of hunger. The guards destroy new structures because they are distracting to it. It is submissive to the sculpture's creator because it perceives him as the ruler of the land it is in.
SCP-121 It is invisible and stuck between dimensions in the sky over the town, unable to move, and is trying to reproduce.
SCP-1178 This is the result of an attempt to kill one, resulting in a being that is a amalgamation of the entity, the people that tried to kill it, and the weapon that they used.
SCP-1926-R is R'lyeh and SCP-1926-1 is Cthulhu. Although the article claims that it is only a prank, the writer of the article has revealed that this is a lie.
SCP-2600-CU is one that causes those under its influence to refer to is a being extremely cute despite the fact that it is really a disgusting Blob Monster and they are fully aware of this. It is mind controlling the foundation into finding it a mate so that it can conquer the planet.
One that is a bit more ambiguous is found in an extremely well hidden story, which you can only find by Going to the page for SCP-000, which isn't on the main list, and then highlighting the blank space below the article. The narrator of this story describes encountering Eldritch Abominations as he wanders through a world of nothingness and, depending on how you interpret the story, the narrator may also be one who was imprisoned by the foundation. Another possible theory is that the narrator is really an AI trapped in the foundation's database.
Whatever is in the Cave of Red Flies from The Wanderers Library (An SCP Foundation Spin Off). It had smooth red skin like that of a frog, had the body of a bare man, legs like those of an eagle, and four crimson-feathered wings. I could not see his head or face, or more likely my sanity forbids me from remembering. But I remember those two great eyes, impossibly large, shining with an intelligence like laughing fire. That's hardly the only example on the site.
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.
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.
Humorously addressed in an advertisement for Elder Sign.
H-M Brown's Shell introduces us to a strange creature that is difficult to describe and has led those who saw it into madness.
The podcast Welcome to Night Vale features plenty of these, most memorably the Glow Cloud: a giant flashing cloud whose colors change depending on viewer, that rains animal carcasses down on the town and possesses Nightvale citizens. It eventually becomes Chairman of the School Board.
And, of course, there's a couple hints that our narrator, Cecil, might be one himself. He's probably friendly, though.
The Non in Dragomirs Diary are occasionally described as things which were not meant to exist. This might explain their shadowy bodies, green eyes, abnormally-powerful abilities, and general weirdness.
The Big Bad of browser game Demon Thesis is one of these, and is responsible for both empowering four college students with Elemental Powers and other spells and creating the monsters they are suddenly forced to defend themselves and others against, all for his own sinister purposes.