And an interesting twist from Night Mare, book 6 in Piers Anthony's Xanth series: the protagonist, Mare Imbri, is a "Night Mare." When, in a climactic scene, she confronts a shape-shifting villain, he almost saves himself by shifting from human form into horse form. Imbri does eventually defeat him, but it becomes much, much harder to do so. It isn't just because she can't hurt a fellow horse either, it's because she's in heat at the time. (Sigh, Piers Anthony...)
In Ursula K. Le Guin's Earthsea story "The Rule of Names", two sorcerers get into a duel involving shapeshifting; it ends with one back in his human form, and the other a dragon. The human says something like, "I'm tired of this; it ends now; show me your true shape, by the power of your True Name." He speaks the Name. The dragon is unaffected, and replies, "That is my true name; this is my true shape." CHOMP!
Red Court vampires can either take the form of beautiful young men and women... or hideous black rubbery bat-creatures. The human form is an illusion, which is bad news for anyone who's infected.
Also, this is explicitly the main power of the Knights of the Blackened Denarii. They change from human into some horrible form for combat, with a twisted Angelic rune on their forehead and a second set of eyes. So far we have seen: A snake-man, a medusa-haired human/panther thing, a six-legged horned fanged bear, a normal human with a shadow that will strangle you, an obsidian statue, a feathery tentacled thing, a praying mantis with little praying mantises for blood, an emaciated grayish spiny humanoid, and various forms of big and ugly and scaly and hairy.
In a subversion, Nicodemus (the head Denarian) explicitly does not have a One-Winged Angel form- both because he's The Chessmaster by nature and would rather put his power into abilities other than raw strength, and because between the Artifact of Doom hangman's noose he wears (which makes him immune to conventional attacks) and his own skill as a warrior, even his base human form can overpowering anything if need be.
In James Swallow's Warhammer 40,000 novel Deus Sanguinius, Arkio starts to metamorphise under the influence of Chaos. Inquisitor Stele can contain it, but at the climax, fighting Rafen, he starts to bleed black blood, and then to change in form. Rafen shows him himself in a mirror and he breaks it in rage. Then the Spear of Telesto rejects him.
There's something of a sort like this in American Gods, as the deities seem to have a form that shows one of their believers whose faith was strong enough to make them real. Thus, Mr. Nancy/Anasi has this form of an African boy with a distented stomach and infected leg and Hinzelmann shows a child pierced by swords, which actually reflects his being created through human sacrifice. Interestingly, The Other Wiki novel for the character indicates that this was actually that character's true form in the original stories.
In the The Dark Hunters series by Sherrilyn Kenyon, the leader of the Dark-Hunters, Acheron, is in actuality an Atlantean god. This means that if he's pissed beyond all hope of redemption, he turns blue, gets black horns, nails, and lips, and rips the ever-loving everything out of most everyone. Bonus points for the ability to end the world should he go visit his mother in Atlantean Hell.
Visser Three from Animorphs used dozens of these over the course of the series, rarely using the same one twice. Fridge Horror ensues when you realize there are species of these for him to acquire DNA from.
Also, you realize just how awesome} V3 is: you can only acquire DNA while in your native form, and while Andalites such as the one the Visser possesses have the slashing tail of doom, that'd barely inconvenience some of the nastier beasties the Visser has turned into - some of whom have projectile attacks like fire and venom and spears. A centaur with a pointy tail managed to get close enough to these things to actually touch. (Yeah, acquiring puts 'em into a trance... but you gotta touch 'em first.) One of them was actually a natural predator of his race, evolved to remove Yeerks from their hosts to eat.
In the finale of book 2, Fablehaven's artifact is guarded by a seemingly harmless cat. When you kill it, it is resurrected as a larger cat. This happens seven more times, until it has become a winged, three-headed, three-tailed monstrosity with snakes sprouting from its back that shoots acid.
When Gavin (a.k.a. the demon-dragon Navarog) scales up into his dragon form.
Melancholia has this forced upon her and it also seems to be the case for people who learn their true names (although physically they don't change at all).
In the Doctor Who spinoff Faction Paradox series, the more the Time Lord Expies regenerate, the more like this they become until they're nothing but sentient masses of weaponry and defensive devices. You wouldn't like to meet 'em.
This is rather in-line with aspects of regeneration dating back to the 1980s in the EU. The novelization of The Twin Dilemma mentions that Time Lords who (for whatever reason) undertake regeneration multiple times again immediately after regenerating, without seeking rest or medical help, run the risk of becoming, with progressive rapid regenerations, eldritch abominations at best. At worst? Sentient goo lumps.
Later novels revealed that the earliest Time Lords with regenerative capabilities sometimes would merge with any nearby biomass when regenerating. This could be as simple as taking on aspects of the last meal they had eaten, but given the right conditions...
Defied in Percy Jackson and the Olympians, in the sense that the Big Bad Kronos is trying to achieve the power of returning to his true form, instead of possessing his follower Luke. But the efforts of Percy, Zeus, and all their allies prevent this effect—and Kronos is so strong even without his true form that we can infer that nothing could have stopped him if he had gone One-Winged Angel. Kronos is never fought in anything but a form which is just as human (not completely human, but definitely not comparable to a the gods and titans like Kronos) as Percy Jackson himself.
Inverted in the last volume of The Seventh Tower. Sharrakor, the shapeshifting Big Bad, opens the final battle in his Nigh Invulnerable dragon form, which the heroes are no match for. Midway through the battle, the sorceress Malen manages to magically force him to take on a much weaker humanoid form, in which he is killable.
Transforming into something stronger one of the abilities of the vampires in Zero Sight where they call it "manifesting". Rei Bathory, the main love interest of the protagonist of the series does this at the end of book two.
The Crimson Shadow: Greensparrow takes on his shared dragon form for the climax of the trilogy.
Several villains in Undefeated Bahamut Chronicle take a large dose of the drug Elixir to turn themselves into Nocturnals, beings that are compared by the narration to demons. They get black skin, white hair and massively increased physical abilities. If the transformation extends to their whole body, it will eventually kill them, overlapping with Deadly Upgrade.