In Dino Attack RPG, the Maelstrom is depicted as being a lot more Lovecraftian than in the video game from which it originated, being a force of utter destruction the likes of which cannot be comprehended by any ordinary person. It cannot be stopped, only delayed.
One (Missingno.) was a failed prototype of the Mewtwo cloning project, fused with a Reality Warping supercomputer that could have made AM proud. Its brother was a Cipher experiment Gone Horribly Right, which was prone to kidnapping innocent newborns and converting them into soldiers for its army.
♀ was a formless mass that emitted a song that caused any being to go near it to be driven into homicidal insanity.
Apotheosis has numerous gods that look eldritch, but the Crawling Chaos takes the cake. It has a thousand eyes, millions of claws, and jaws the size of worlds. When an old man summoned it in an accident, his eyes and organs were liquefied.