The Insidious Bogleech uses the idea frequently (albeit buried among many, many examples of simple Our Monsters Are Weird). In Mortasheen series of monsters, everything under the Unknown section is styled this way, from the Vault (which can go through solid matter like it was nothing and is spawned from Alien Geometries) to the Lobotomask (a horrible face-type thing that eats your mind).
The Cultists in 8-Bit Theater worship and summon eldritch abominations on a regular basis: first, there's a nameless creature referred to as an "eye-stalk" which mind rapes anyone that makes eye contact with it (in addition to transporting the victim to its own pocket dimension). Then there's major enemy Ur/Jnn'efur, who fits the "fragment of the true being" bill.
Endgame enemy Chaos is definitely this.
El Goonish Shive has the eponymous "whale" of the January 2013 story arc. It's simultaneously of and NOT of our reality, and it's even depicted in a very odd way compared to other characters. However, it and its kind appear to be benevolent, and feed on excess magic energy in an area, keeping it from going out of control. They admit they're more similar to bottom-feeders in this respect, but prefer to be called whales. "We like whales."
In the actual webcomic, it is revealed that there are extra-dimensional horrors scary enough to dissuade even Mad Scientists as reckless as the Heterodynes from messing with time. When time is disturbed, they notice. The above picture is of them. The Castle also mentions that's not the first time they show up, though last time they were much smaller and had brought hats. Which later leads to the revelation that those exact smaller, hat-wearing, tangential-to-time eldritch monsters might be under Wulfenbach employment.
Coyote is a phenomenally powerful Reality Warper, even by the standards of a setting where magic and magitek is everywhere, who casually plucks the moon from the sky and doesn't even maintain the same shape between panels. When Annie sees Coyote in the ether he can best be described as a starry night sky with lots of teeth and eyes, and she rightly describes him as "magnificent and terrifying".
Jones a.k.a Wandering Eye is the oldest, most bizarre and mysterious creature on the planet. "Creature" because they aren't really alive, being immortal, indestructible, and unchanging since the very first second of their existence, "oldest" because their existence began 4.5 billion years ago (and they remember every second of it), and "mysterious" because not even they have the slightest clue what they are. Annie's reaction to learning this is priceless.
Guttersnipe features H.P. Lovecraft as a sort of 1920s Stephenie Meyer, complete with eldritch abominations standing in for sparkly vampires.
The Horrorterrors of the Furthest Ring befit the classic definition of vast monsters of varying forms of hideousness and deformity, with plenty of tentacles. There's probably hundreds of them, arranged in several tiers of power, the strongest being the Noble Circle of Horrorterrors. They can communicate with the Derse dreamers of every session of Sburb and are intended to provide some level of guidance. In the kids' session, Rose - previously well-read in their lore - channels their power through her Thorns of Oglogoth and it proves to have a less-than-desirable effect on her sanity.
Feferi, one of the trolls, was raised by one. It once provided the image for this page.
Feferi's lusus is capable of killing every troll in the Universe with a sound. And she's an emissary of the Noble Circle of Horrorterrors, implied to be a lesser version.
Lord English, the thing that is killing the Horrorterrors, is a time-traveling demon who feeds on dead universes, and has lived through every universe, ever. Then we find out he's just another player in the game.
The Denizens are beings that act as the boss of each player's personal planet and are responsible for creating most of the enemies in the game that are not Carapacians. However they are far more than just ordinary Sburb NPCs. They posses knowledge of events in other timeless and are even able to affect events in other timelines, and it is in fact implied that each of them is the same being in every version of Sburb in every timeline and not just parallel versions of each other like other recurring Sburb characters. Most of them look like gigantic snakes with faces that shine like suns. Each of them speaks in a Starfish Language that can only be understood by players that were assigned them. Several of them are named after gods and monsters from Greek Mythology, many of which are also listed in the section on Religion And Mythology. The most powerful of them all is Yaldabaoth. They are not good or evil, as it normally isn't actually necessary for the players to fight them and if the player does not attack them they offer players a choice which helps them towards their destiny, although they are just as willing to help evil players as good ones.
Several instances in Kidd Commander. Besides the "Elder Gods"? There's a panel or two with "Queen" Hastur, the least cruel of the known Elders, and one of the smaller ones. When she showed up, the sky bled.
Exris from Monster Lands is a shadow inside a robe whose only features are his white eyes and jagged teeth, which seem to be floating around inside his body
Gravehouse of Necessary Monsters turns out to be much more tentacle-monstery than the human he looks like. ("I crawled into his body and ate him up from the inside out. Until all that was left was skin and memory. Tell me... would you like to meet the real me?")
Wonderella: Meet Spirral. Duder's a 300-story thingy who travels the galaxy, mind-controlling millions with his Spirral Spores.
The Order of the Stick: The Snarl is an incomprehensible being born from deific rage and strife, kept in check from destroying the world and the gods only by five one measly gate. He's depicted as nothing but lines of blue and purple energy in a very vaguely humanoid form.
In The Salvation War setting, according to Word of God, whatever lives on the opposite side of the Minos Portal in Hell (the portal through which the human dead arrive in Hell) exists in a reality so different and alien that nothing from either "Universe-One" (Earth) or any of the "Universe-Twos" (Heaven, Hell, and other assorted "higher-level" realities) can exist on it. Nothing either living or mechanical from either set of universes that passes through the portal has ever returned.
Schlock Mercenary has the Paa'nuri (with a mobile apostrophe), entities made entirely of Dark Matter and only detectable by traditional matter through the gravitational disturbances they generate and also used as weapons. Only ever "seen" on a gravy-screen, where it looks like a mass of tentacles the size of a planet. It's implied by one joke that either their term for other races translates directly as "annoying" or they don't actually have a word for other races and just call them annoying.
Shadowgirls takes direct inspiration from Lovecraft for its portrayal of the occult, most obviously in the character of Mother Hydra.
Darumatha, the Demon-Dragon of Broken Hours (with a name like that...) in The Water Phoenix King. It might appear in the form of one of your dead friends, fatal injuries and all, or it might take its real form of a vast serpentine coil of living metal scales, fangs, and spikes reaching all the way to the outer stars, a manifestation capable of making strong men vomit in terror, or as a charming young woman in an evening dress who prattles cheerfully on about cutting hearts out. Or just go back and forth between all these shapes, apparently at random.
In the webcomic Wildlife the protagonist is one of these.
Incubus Tales features recurring antagonists known only as "Abominations", which are said to be anathema to everything that is not them. They have been shown to take a variety of shapes and forms, all of which are appalling and traumatic to everything and everyone around them. One of the most prominent, the Lord of Abominations, was so monstrous it was not shown and may have been incomprehensible.
Secret:[looking at a mural] What are these, Misho? Misho: Mostly, they're images of the primordials, as they were before the war. The gods felt it important we be reminded who we were fighting... thought we would feel a bit more confidence if we knew the nature of our foes. Secret: Who's that? Misho: That would be Adrián, the River of All Torments. The gods weren't... used to humans, at that point.
This quote sums up the "Botfly," or the "Green Lady," a bizarre time parasite that travels through time and breaks reality. The best glimpse we've ever gotten of it is a horrifying, blurred out, tentacled monstrosity that follows Bina closely. When she turns around, it turns into a television, preventing us from witnessing the true horror.
Apothecia has the alien that Jesse meets, which can best be described as a writhing, fungal stew with More Teeth than the Osmond Family and eyes and Blue and Orange Morality that makes killing things as important to it as breathing is for us.
In DeepRiseThe Nobles build their cities around huge sleeping things that emit a steady stream of heat, radiation and other useful things.