While we don't know much about them yet, The Hunters Three of the relaunch Animal Man appear to be these. Three absolutely horrific creatures who "disguise themselves as men". According to interviews, the three of them are from the edges of the DC Universe and serve a dark force lurking beneath it. Though, really, their appearance says it all.
Atomic Robo had to fight an extradimensional Eldritch Abomination once - or four times, more accurately. Not because it kept coming back, but because it existed simultaneously across several points in space-time.
The Authority once faced "the closest thing to God this Solar System has ever seen". It was so big that Carrier, a city-sized spaceship, could travel its circulatory system like a bacteria travels ours and old enough that his parasites evolved into a civilization. This monster was responsible for Earth's creation and lived on it for some time. When he came back, he wasn't pleased to find out that his planet had new tenants.
The Lost Year miniseries also dealt with the Authority ending up in a universe without superpowered beings and trying to figure out why their powers were wonky. As the Doctor put it, they'd ended up in a universe where Lovecraft was right — the earth was in thrall to a cosmic parasite that lurked in the back of everyone's minds. And the Authority's presence just woke it up.
The feeding of said parasite caused a lot of problems for its victims, with many people suffering headaches, nausea, irritation, exhaustion, and general misery, with occasional people committing horrible acts or even suicide because of the thing's presence. Did we mention this world was exactly like ours? Commence paranoia now...
The super-organism in Bio Apocalypse has a habit of spawning these and might even qualify as one itself.
One played a major role in Cyborg's origin in the comics. While visiting his parents at S.T.A.R. Labs, Victor's mother Elinor accidentally activated the experimental dimensional portal device his parents were working on at the time. The... thing that came through it immediately devoured his mother and mutilated Victor before his father Silas forced it back into its own dimension, but not before the creature gave him a terminal case of radiation sickness. Silas barely managed to save his son using cyborg prosthetics of his own design, but Victor resented him for turning him into a "cyborg freak" for years, believing that his father wanted to experiment on him, until Silas revealed that he was dying thanks to the radiation. This led to Cyborg getting over his bitterness towards his father, and they spent one last day together as father and son before Silas died.
The Flemish comic book series De Rode Ridder features an eldritch abomination in the album "De Rode Herberg" ("The Red Inn"). Said creature came to Earth in a meteorite and took up residence in the eponymous inn, feeding on people that spend the night there.
One Donald Duck issue revealed that a giant octopus called Ar-Finn sleeps beneath the depths in a sunken city (Cthulhu and R'lyeh, anyone?). Our reality (or at least Donald's) exists only because Ar-Finn dreams about it. If he wakes up, the world will start to adapt to his image, with the architecture becoming more and more alien and the people more octopoid in appearance. It was awfully cynical for a Disney story, especially the ending, where Donald is horrified to find out that our whole existence is just a dream. Probably as close to Lovecraftian standards as Disney will come for the foreseeable future.
"Them" from El Eternauta easily come off as this; the best description we are given is that they are the "cosmic hatred".
Caged Demonwolf from Empowered is an extradimensional Energy Being so powerful that, before his sealing, not even the A-list supers could stand up to him.
The DCU 52 miniseries introduced the Four Horsemen of Apokolips: ancient, primal entities that hail from Apokolips and predate the New Gods. They are limited only by their inability to physically manifest in the universe without assistance. In their debut, using flawed bodies that could only channel a fraction of their true power, they devastated Kahndaq, murdered Black Adam's new family, and nearly killed Black Adam himself. Thankfully, they are now Sealed Evil in a Can... inside Veronica Cale.
Furthermore, 52 featured the evolution of the villain Mr. Mind, who became a cosmically huge insect abomination. He's responsible for the differences between the 52 realities of the DC multiverse, having eaten key moments in time from all but one of them.
The 5th Dimensional Imps, of which Superman villain Mr. Mxyzptlk is the most famous, have become an example of this. They can more or less wear the laws of physics like a funny paper hat, and while they tend to appear as cartoonish characters, those aren't their true forms. Luckily, most of them aren't interested enough in meddling with our universe, and those that do are permitted only to cause mischief. Sometimes hiccups occur, like the time Mxyzptlk made the well-intentioned mistake of giving his reality-reshaping powers to the Joker.
It's eventually revealed that there are even higher dimensions than this, each with their own imps. The higher the dimension, the stronger the imp, all the way up to the one and only tenth-dimensional imp, Ultimator. He looks like this◊.
One of Alan Moore's early works is Whatever Happened to The Man of Tomorrow?. It's set in an alternate possible future where Superman is getting ready to retire - up until all his enemies return, and all-out war between them and his friends (with Lois, Lana, and Jimmy taking up the Phlebotinum behind some of their one-shot powers from Silver Age stories) It's a brutal affair where people die and From Bad to Worse reigns supreme. Then he puts together the clues of what's really going on. It turns out: Myxy orchestrated all of this. As a superdimensional imp older than time, is now bored with being mischievous; every so many millennia he reinvents himself. He was benevolent once, more recently a harmless trickster, but now? He wants to "try being evil for a while; maybe after 2000 years or so of that, I'll get to be guilty". When he drops the Goth version of his usual little-guy-in-Nice Hat image - mocking the idea that a sorceror from the fifth dimension would really look like that - he appears as a jagged-edged humanoid tear in space with malevolent eyes and maws, and Lois points out for the benefit of us readers that it hurts her eyes just to try and look at it, like all the angles are wrong. Now THAT begins to approach the idea of a being from the Fifth Dimension.
In one issue, Superman teleports to the Edge of the Universe. Way out there, space becomes white, and after that, there is a MASSIVE, INFINITE WALL of Eldritch Abominations / Body Horrors marking the final boundary between our universe and the next one over. In Countdown to Final Crisis, though, this wall has symbols and statues of humanoid figures on it, like it's the outside wall of the Monitor's base.
This Source Wall lies on the edge of the known universe, in the Promethean Galaxy. Beyond the wall lies what is known as The Source, a cosmic essence or being that is the "source" of all that exists. The wall is theoretically passable. However, all those who try have been inevitably trapped in it. Over time, it has been made up of the bodies of would-be conquerors and curiosity seekers from all across the universe.
JLA: Another Nail has the Limbo Cell, a primordial creature that eats existence.
In Ghostopolis, any living person who ends up in the titular city has the potential to become this.
He used another member of Starro's species simply called the Star Conqueror during his run of JLA. It had a different color scheme and was much bigger — like Hudson Bay bigger. In its second and so far final appearance, it invaded the dreams of the American populace, putting to sleep and taking control of nearly everyone in the entire country. It took a two front assault on the creature — some of the remaining JLA members attacked its physical self while the Lord of the Dreaming aided the other JLA members in attacking its mental self — to stop it. It was finally driven off into deep space while its mental self was imprisoned in the Dream Lord's chest.
Mageddon, the Big Bad of his JLA run, is a cosmic doomsday weapon that survived the death of the universe of the god-like beings who built it. Its purpose is to initiate universal suicide by psychically prompting all living beings to war with each other to death. Even when disabled (by the combined forces of the angelic hosts of Heaven, every single human being on Earth endowed with super powers, and a secret weapon that was its Kryptonite), it was still in danger of detonating and vaporizing half the galaxy. All while being far larger than the Earth.
The Archons of The Outer Church in The Invisibles are typical Eldritch Abominations — slimy, chitinous, and decidedly non-human. In an interesting inversion of Lovecraft's themes, the Archons aren't entities of entropic chaos, but absolute order. When the universe reorients itself in their presence, it's not because it's breaking down, but because it's coming more in line with the Archons' specifications.
His run on Doom Patrol was practically made of these. Orqwith, a city that doesn't exist and sends out Scissormen to cut people out of reality as we know it. Red Jack, who lives in a pocket dimension mansion with a floating head that is just a mask and claims to be both God and Jack the Ripper. The Fifth Horseman of the Apocalypse, Extinction and Oblivion, who lives inside a painting that can 'eat' reality and is gigantic with no skin. The Decreator, some kind of anti-god that appears as simply a gigantic eye in the sky. The Avatar that lives under the Pentagon appears to be this, although we didn't get to see too much of its full extent, but required Flex Mentallo, who can warp reality by flexing his muscles, to force the Pentagon into a circle, which caused an immense amount of strain, and the summoning of The Candlemaker, a far worse Eldritch Abomination, to stop it.
The Big Bad of Morrison's run on Action Comics is Vyndktvx, a 5th Dimension Imp, like Mr. Mxyzptlk, only a psychotic mass murderer rather than a practical joker.
The recent run on the Green Lantern comics has seen various alien entities that are incarnations of the various colors of the emotional spectrum, which has led to some fan speculating that these beasts may be like infant Chaos Gods from Warhammer 40,000 in training. These include the Yellow Entity Parallax (Fear), the Green Entity Ion (Will), and the Violet Predator (Love). These entities are known to possess and empower worthy individuals, but are often monstrous and insanely powerful.
The Orange Entity Ophidian (Avarice) was confirmed by Word of God to be the voice within the Orange Lantern Battery that converts its wielder into Agent Orange. Atrocitus initially assumed The Spectre, the agent of God's Wrath, was the Rage entity. The Spectre denied this, claiming that he has met the Rage entity and warning Atrocitus (who, as one of the Five Inversions, is himself a Humanoid Abomination even without his red power ring) that seeking it out would only lead to his destruction. Avara, the Blue Entity of Hope, looks like a huge eagle... with three faces and beaks; while Proselyte, the Indigo Entity of Compassion, is just a massive octopus. Presumably, he just wants to hug you.
Butcher, the Red Entity of Rage, is a bull.
Nekron, the Guardian of the Black Lantern Corps, whose plan is revealed to be killing the Entity, the being of White Light that gave birth to all life, and, as a result, kill everything in a instant. The moment he dealt the first blow, we know he meant business. And he was created by the darkness preceding the universe.Nekron is such an Eldritch Abomination that he can't even exist as a physical entity. He needs a tether for that, which comes in the form of the necrophilicherald of death, William Hand. This only works when he's dead, however.
Later villain Mary Shelley Lovecraft, a metafictional entity who seeks to tear down the walls between "ideaspace" and reality. Intentionally or not, her mere presence in a reality causes stories to blur together (while in the Lovebunny Universe, the events of Lovecraft's The Colour Out of Space occurred, and while in the Archie Comics-inspired town of Haverhill, "The Shadow Over Haverhill" happened, with some Frankenstein thrown in for good measure). The only reason Cassie and Vlad managed to (temporarily) kill her was because she was severely weakened due to a confrontation with a shitload of superheroes (despite taking place in some kind of void, the power she exerted in that battle was able to reach the Hack/Slash Universe and cause every holiday-themed slasher to come out of hibernation early).
The Ogdru Jahad, neither male nor female, sleeping until they bring the downfall of man. They have an army of frog men that have long, clinging tongues capable of sapping the prodigious strength of Hellboy, let alone a human, can take on the appearance of a normal human being, possess Genetic Memory, and have the knowledge of great spells of power not heard on the Earth for millions of years. Also, every single frog man is a human infected by the Ogdru Jahad.
The Ogdru Jahad's most powerful servants are the Ogdru Hem, 369 lesser abominations, each incredibly powerful in their own right. These include Sadu-Hem, the Conqueror Worm summoned by Von Klempt, and the discorporated entity that possesses the ectoplasmic medium Mr. Tod when he goes off "fishing in the deep-end".
Additional Ogdru Hem show up in B.P.R.D.—Katha-Hem, who ravages the central United States, and the unnamed creature in the Salton Sea, breathing the upgraded form of the Frogman Plague into the atmosphere.
The Moose from Johnny the Homicidal Maniac looks like this trope, and its initial appearance screams this as it tears through Johnny's Torture Cellar, killing everyone, and apparently destroys reality upon reaching the surface. Despite this, however, it's later revealed by the Devil that its origins are closer to that of The Heartless: it's an accumulated distillation of negative psychic residues created by humans behaving generally badly.
Starro, the very first foe they dealt with, slowly moved in this direction over the years, being a literal Starfish Alien that latches onto you and takes away your free will, though there was recently revealed to be a humanoid alien controlling the giant starfish "Starro" that the Justice League faced in the past. The humanoid alien has a smaller starfish on his chest. He controls the Starri from that.
The ultimate would be the Anti-Monitor, the Big Bad of Crisis on Infinite Earths. An Energy Being composed of pure anti-matter on the inside, covered by a giant armored shell that serves as an energy collector to gather positive matter from the universes he wiped out. At his strongest point (when he traveled to the beginning of time), a coalition of heroes from many universes and time periods didn't even scratch his armor. He was eventually killed by being magically poisoned, being attacked with the power of a star, attacked by two parallel universe Kryptonians, hit by Darkseid's full power, and finally thrown into a star, but that didn't stick. It took a duel with all the Guardians of the Universe and a galaxy-wiping explosion to take him out a second time.
Another Abomination is the baffling entity known as the Overmonitor or Overvoid. It's a sentient void, inside which the entire DC Multiverse exists. It created the Monitors, and it's heavily implied that both the Monitor and Anti-Monitor were born from a probe it sent to investigate: meaning it's responsible for two eldritch abominations already. And, even weirder, it's described as being the embodiment of the very concept of the narrative.
Darkseid also becomes this during Final Crisis; after his reincarnation into Dan Turpin, his presence actually starts to decay time and space. Mandrakk is using Darkseid's attack to hide his own plans (but is stopped before getting too far). How does Darkseid break reality (one parallel universe actually is destroyed by this)? He sits on his throne, waiting for reality to die merely because he exists. Awe. Some.
Imperiex could also be considered one, given that it was the power of the Big Bang given form who sought to reboot the universe due to an impurity in the fabric of existence that it detected. Ironically enough, that flaw was Imperiex itself. It proved to be enough of a threat to force Mongul II and fucking Darkseid to ally with Superman and the rest of the resistance force. One of his most immense displays of power was reducing Doomsday to a skeleton in one shot. He was finally destroyed by a sun-drenched Superman after an enormous battle, though not before killing off a good portion of both the resistance force and Earth.
Though, in appearance, they are standard angels and demons, many of the characters of Lucifer have powers and attitudes that are more in line with this trope. At one point, Lucifer flies out to just in front of the Source mentioned above and ignores it. It's simply beneath his notice at the time.
The same series has the Jin-En-Mok and the Silk Man, survivors of the destruction of what's described as "an earlier, cruder Creation" and so very horrible in their own, special ways.
In the Marvel Universe, there are various 'Elder Gods' that count. The most notable of these are Chthon and Set.
Dormammu and Shuma-Gorath aren't 'Elder Gods', but far, far more powerful and ancient multiversal threats. The most powerful known regular demon lords are supposed to be as insects to them (and so would Chthon and Set).
And Dormammu in turn is more or less an ant compared to Shuma and his fellow Many-Angled Ones, the likes of whom are only a step or two below the Living Tribunal each.
Zom, while not a true Eldritch Abomination in the sense that he was created, still arguably qualifies. He's an ancient living weapon with unspeakable power sealed in a magical amphora that Strange has to let out to have any hope of defeating Umar. It works, scaring Umar (a Humanoid Abomination with near-godlike magical power nearly on par with those of her brother, the aforementionned Dormammu) shitless, and it takes the Goddamn Living Tribunal itself to put him back. Later on, during World War Hulk, Strange imbues himself with some of Zom's power and proceeds to beat the shit out of the Hulk before getting distracted.
Galactus. Older than the universe itself and incomprehensible by mortals. It's canon that his hat-wearing humanoid form is simply an image our puny minds superimposes over a reality we cannot truly comprehend; for instance, Beta-Ray Bill's species sees him as a big starfish.
Although he's a mechanical example, Ultimate Gah Lak Tus definitely qualifies. Aside from driving everyone who sees it insane and spreading a flesh eating virus across the planets it consumes, much of the devastation it causes stems from its own gravitational pull.
Mephisto qualifies as this. Sure that he may look as a red-skinned vampire, but that's just his most common form. In reality, Mephisto is an inconceivable emboidment of evil that rules a part of Hell's plane of existence, and he has gave a taste of what he truly looks here◊!
It's actually implied that he might not have any form at all. Also, he's a semi-subversion in that while he likes to act like he's a big deal, he's a lightweight compared to Set, Chthon, Dormammu, and the other really nasty beings out there.
The Other. True to its name, The Other is an Eldritch Abomination that is so other that it cannot be perceived by even the most powerful abstracts in existence; it is also incapable of manifesting its true form, provided that it actually has one, in our reality. It must instead use projections of one or more physical entities such as The Greys or a colossal human hand with two large starry eyes on its palm that may or may not actually exist in order to interact with our reality.
In the recent Realm Of Kings one-shot, Quasar visited an Alternate Universe which was apparently sold to Dark Gods. Not only does everybody in this world carry an Eldritch Abomination inside one's body, but the whole UNIVERSE is also one fricking Eldritch Abomination. It turns out that the whole thing started when somebody who turned out to be Captain Marvelkilled Death in this universe, which caused life to grow unfettered... and turn cancerous.
Quasar: I see it now! I see it all! Their universe! Disgusting! An abomination! Pulsating with corrupt life! One giant, twisted organic mass! Their whole universe is a deathless corpse! A cancer trying to metastasize into our reality! I asked: what’s the worst that could happen? This is. How can I protect the universe from another universe? Galaxies and worlds all united to consume us?
The Thanos Imperative event is about said universe finally flooding into the 616 proper. Just to give you an idea of how terrible this is, not only has Galactus joined the resistance, not only have the freakin' Celestials joined the fight, but the Guardians of the Galaxy are forced to recruit THANOS to have any hope of winning in a universe without death. It's especially unnerving since this essentially makes Life itself an Eldritch Abomination. When one thinks about it, it's an invasive species writ large (without death, there was no checks on the growth of life; without checks, life began to absorb everything into itself...).
From the Incredible Hercules event Chaos War - Amatsu-Mikaboshi, CHAOS KING. Like Galactus, he comes from a Universe that was before the current Marvel Universe — or rather, he was that universe. He's Anti-Eternity, Evil Twin of Eternity, Anthropomorphic Personification of the Universe itself, an ultimate force of destruction that will not rest until the Universe is destroyed and nothing aside from him remains. And he can squish All-Father level gods like they were flies.
The Chaos King's army is composed of deceased gods he murdered and recreated as his puppets. But one of them is Glory, a gigantic monstrosity composed of thousands of alien pantheons it assimilated into itself. Its nature is so alien and bizarre that even The Mighty Thor was scared beyond words during their encounter. It's an Eldritch Abomination even to gods. It's also one of the few beings that joined the Chaos King willingly, because it enjoys all the destruction he causes.
There are also The Infinites, a trio of immense beings who traveled the multiverse realigning the energies of universes in a way they considered harmonious. They were so big that one of their hands was larger than a galaxy. It took The Avengers summoning Eternity, the living embodiment of the Marvel Universe, to face them. When they learned that their actions were causing the deaths of countless beings, they were horrified and abandoned their experiment and began to make amends throughout the universes they visited.
Thanos and Galactus also once ran into a being called the Hunger, which operated on a universal scale. It was to Galactus what Galactus was to human beings. It was depicted as a gigantic black void with glowing eyes of fire, because nothing else could portray a pit where existence ceases. Thanos managed to prevent his arrival in this universe, and cut off a piece of the being, which withered and died. But it's main body is still out there.
Also in Marvel, the entity Sublime, introduced as Dr. John Sublime in Grant Morrison's run on X-Men. The last storyline of that run was Here Comes Tomorrow, replete with imagery straight from the Book of Revelation in The Bible. Sublime isn't John Sublime, he (it?) is a three-BILLION-year-old sentient strain of bacteria that wants to stop evolution, or else control it, so life that it can't infect and possess can't survive long. Sublime loathes mutants because they're intelligent enough to fight it and naturally immune to possession except through work-arounds like the super-steroid Kick. Its influence (personal hypothesis here) may very well be a major reason why the X-Men can't ever catch a prolonged break. In Here Comes Tomorrow, Sublime (its core cells possessing Dr. Henry McCoy) seeks to wrap its flagella and pseudopods around the full power of the Phoenix Force, so it can "remake God in [its] own image." That timeline ended up getting BURNT OUT OF EXISTENCE by Jean Grey as The [Messianic] White Phoenix of the Crown. Revelations in various other titles indicate that Sublime was responsible for Weapon X (if not the ENTIRE Super-Soldier program), and after John Sublime died, Sublime was still the Big Bad the events of Phoenix: War Song, its minions oversaw the creation of the Predator-Xs, and various other nasty schemes. Oh, and note how Sublime's core cells got in possession of John Sublime—it infected a Wolverine from another alternate future (Weapon X: Days of Future Now) while his mind was being projected back by Rachel Summers into his past self to alternativize that Days of Future Past retread.
Brian Wood's new X-Men series has Sublime joining forces with X-Men against Arkea - another sapient strain of bacteria that Sublime kicked out of the planet billions of years ago. It evolved in space, gaining power to infect machines like Sublime does organic beings and wants two things - revenge and infecting everything on Earth. It's more powerful and advanced, but also more primal, lacking her brother's subtlety, it just destroys.
The Phoenix Force itself, in many ways. While not strictly benevolent or malevolent - it simply doesn't really get humans, and its experiment of being one rather backfired, leading to the Dark Phoenix - as shown in Avengers Vs X Men it has a penchant for eating stars/planets to maintain its energy. This was particularly displayed when Thor managed to hurt it in deep space, smashing it halfway across a solar system. This turned out to be a case of Nice Job Breaking It, Hero, as the Phoenix promptly ate the nearest planet. The Worf Effect ensued.
It ticks all the boxes, particularly in the Bring My Brown Pants department - something not unjustified by the Dark Phoenix incident, which caused a planetary level genocide and nearly inspired an interstellar war.
And from Young Avengers vol.2 we have the Big Bad, Mother - a parasite from another dimension, who feeds on powers of reality-warping children (only this kind of power can hurt it, but kids aren't experienced enough to consist a challenge for it). It's abilities allow some really freaky transformation, as well as power to warp reality around it, taking control of adults, obscuring themself from he eyes of those who are strong enough to resist mind control, and transforming things into bizarrely creative way with a bit of meta touch (it once trapped Billy into an empy panel frame). It's home dimension is an Eldritch Location on itself. It's currently usig form of Teddy's death mother. Oh, and at one point it eats the narrator, while he begs readers to save him.
Patriot Costume may be this - nobody knows where it came from, why it took the form it did, why it kidnapped Speed and what it wants from Young Avengers. However, it seems it can freely walk in and out of Mother's home dimension and don't get attacked. It seems to even creeps out Mother a bit.
The unfinished miniseries A Nightmare on Elm Street: The Beginning would have revealed that the Dream Demons, the masters of Freddy Krueger and the ones who gave him his powers, were something akin to this. For those interested, the script for the issue that explored their origin is available to read here.
M'Gubgub from Nth Man: The Ultimate Ninja is a galaxy-devouring abomination with a million forms that has to spread his mass out over hundreds of light-years just to prevent his gravitational field from collapsing on itself. It wants to destroy the Earth in order to eliminate a temporal anomaly there.
"This is but the merest pseudopod of my being! A single follicle protruding from a minor pore! I exist simultaneously in countless forms, stretching out beyond your planetary system into the cold barren emptiness between the stars."
Many antagonists (especially Bigger Bads) from 2000 AD's Sláine fall into this - notably, Crom Cruach/Crom Dubh, the patron god of Slough Feg and Medb, as well as Aten (yep, pharaoh Akhenaten's monotheistic sun god), who Fomorian lord Moloch tries to summon to Britain through child sacrifices. Speaking of Fomorians, they are a whole species of humanoid abominations (except for their sea-demon cousins led by Lord Odacon, who are puppeteer parasites who look equal parts deep-sea monstrosities and aborted hell-larvae); there are also the pre-human gods called the Cythrons, and the Els, who inhabit the various otherworlds. Those races tend to be very unfriendly towards humanity.
The Warren Ellis comic Supergod opens with three astronauts returning to Earth having... merged into a cosmic consciousness thanks to exposure to space spores. Their very presence triggers reverence in the scientists observing them, and they seem to operate several levels above humanity. This triggers a superhero arms race amongst the nations of Earth that eventually results in humanity making their own Great Old Ones, which goes about as well as you'd expect.
It's implied that Sethe and abovementioned The Hunters Three serve the same dark forces.
Another, far earlier one from Swamp Thing, spawned yet again from the brilliant-yet-deranged mind of Alan Moore, is the Original Darkness, the Big Bad of the "Murder of Crows" arc. For starters, this thing is the chaos that existed prior to the Presence beginning its creation. It's also brain-meltingly enormous; the telepath Mento actually starts foaming at the mouth trying to comprehend the scale of this thing. Just having your existence acknowledged by it can have fatal results for even powerful magic-users, as Zatara and Sargon found out the hard way. Oh, and it's absolutely unstoppable; Etrigan, Doctor Fate, and The Spectre all try and fail horribly to halt its assault on Heaven, with the Spectre memorably being curbstomped by the Darkness's thumb. It takes the Presenceitself to intervene to stop this thing, and it couldn't destroy the Darkness, merely nullify it, as they are equals. Long story short, it's likely more powerful and eldritch than everything else on this page put together.
In the end, both the Hunters Three and the Rot are subversions. The Hunters Three turn out to be ordinary people after Maxine frees them of their corruption. The Rot itself is actually the natural force of death and decay corrupted by Anton Arcane, an all too human villain.
Some of these were responsible for Ramjet's Lovecraftian Superpowers in the Transformers comics. A servant of Unicron, Ramjet ended up in the creatures' world when his master imploded, and he was unmade and remade a few times by the creatures for fun, and when they got bored with him, they dumped him back on his homeworld.
From V for Vendetta comes the omniscient supercomputer FATE, which is worshiped as a living goddess by the fascist dictator Adam Susan. At first glance, it simply appears that Susan is insane and thinks the computer is alive, but then you think... what if it is?
Rat Man is primarily comedy, but one early story had "Cosmicus", a Galactus expy starting to devour the Earth... until from the cracks in the ground sprung thousands of tentacles that began to assimilate Cosmicus in seconds. Only one eye of the mysterious entity was seen, and the narrator stated that this being was as old as the Earth (and implied to be Earth itself), and that the all-powerful Cosmicus was only a part of a far greater food chain. This counts as both Deus ex Machina and Big Lipped Alligator Moment, since the entity and all of its implications were never mentioned again.