In Amulet, this happens to anyone who gets "devoured" by the amulets. So far we've seen Luger grow into a giant troll-like creature.
Angel: Illyria transforms into her true form and tries to destroy all existence.
Set, the Big Bad of the Atlantis Attacks crossover was an odd case. An Eldritch Abomination who usually appeared as a colossal seven-headed serpent, he was usually hideous enough. However, when he was fought in his home dimension, he was seen in his true form, and was even more horrifying, resembling his usual form turned inside-out with a grotesque, vein-covered membrane instead of skin.
There are many mutants in the Marvel Universe who can transform, some of them really transform into ugly, instead of cool or powerful ones. The morlock Scaleface for example was a normal woman who could transform into a giant lizard.
There was also Freakshow from the run of Excalibur set on Genosha. He was able to transform into various monstrous forms.
Batman villain, Scarecrow, is definitely one of these as Scarebeast.
One of the EGM Hsu and Chan comics has the title duo getting roped into a wrestling match against Satan. He initially appears as a long-haired blonde in a white suit, but when the match begins, he reveals his true demonic form...a skinny, red-skinned guy with horns and pantaloons, not unlike Pitch.
Jean Grey's Dark Phoenix in The Dark Phoenix Saga may count as well. While wings are pretty standard for Phoenix nowadays, Dark Phoenix's fiery, psychic energy wings and her tendency to eat stars when she's hungry certainly qualify her for a number of things.
In the Crisis Crossover starring Onslaught itself, he took three forms. The first was armor patterned on Magneto's with Spikes of Villainy added, completely encasing a body with the size and musculature of the Hulk. In the second form, the armor was the same, but adapted for a body that was now even larger, but more low-slung with much bigger forearms, and a bony face was visible, and balls of pure energy leaked out of his back and vents in the armor. His third form was disembodied pure energy, and he was defeated just pages after taking this form.
In Megalex, evil and beautiful Sapient Ship personality Shalise transforms into an absolutely terrifying monstrous version of herself. Her mouth fills with fangs, her ears become bat-like, she grows in size, and worst of all, her beautiful breasts become pendulous and rotten, tipped with corroded metal blades.
The Sentry when he becomes the Void, especially in Siege.
Issue #10 ends with Neo Metal Sonic using the Master Emerald's power to become Master Overlord, as whom he fights the Resistance in Issue #11.
At the end of Issue #28, Zavok changes into his giant form from Sonic Lost World, setting the stage for the climax of the entire Metal Virus Saga in Issue #29.
The Clown, a major enemy of Spawn, spends most of his time in the mortal realm disguised as a short, overweight circus reject. But piss him off, and he'll reveal his true form — the large, powerful demon known as the Violator — and deliver a No-Holds-Barred Beatdown upon your ass.
The Ultimates: After The Liberators are defeated, Loki finally decides to get serious and unleash his might. Curiously, it isn't Loki himself that changes form, but the invocation of his full strength bends reality itself around him, turning the sky blood red and summoning an army of mythical monsters to destroy The Ultimates.
Mister Mxyzptlk does this in Whatever Happened to the Man of Tomorrow?, the final appearance of the Pre-Crisis Superman. ("Did you honestly believe that a 5th Dimensional sorcerer would resemble a funny little man in a derby hat?" laughs the villain.) Mxy's true form, being five dimensional, cannot be fully comprehended by earthlings; as Lois puts it, "I can't describe what Mxyzptlk then became. He had height, width, depth, and a couple of other things, too." To the reader, his true form resembles a giant, red and purple demonic humanoid with creepy long arms and an elongated skull, surrounded by weird fractals.
Wonder Woman (1987): When the White Magician learns that Artemis is coming to confront him he uses the new powers he's gained from a deal with a demon to drain lifeforce from his assistant and Cheetah, who he had captured, in order to twist his physical form into a towering musclebound demonic thing. He ends up beating Artemis to death in their confrontation, but his own body burns out and he dies as well leaving only ashes behind.
X-Men villain Bastion has his own One Winged Angel form at the end of the X-Men: Second Coming event. He doesn't last long once Hope Summers gets well and sufficiently pissed.