In the Teen Titans: Trouble in TokyoOAV, the human bad guy leaps into a tank of magical ink, turning into a giant inky monster with metal tentacles, constantly spawning four-color minions.
A few characters on The Powerpuff Girls pulled this trick. In the episode "Knock It Off", for example, Professor Utonium's slacker roommate from college, Dick Hardly, gets some Chemical X and starts making hordes of Powerpuff clones, renting them out to big cities as a new crime-prevention system. When the Girls learn about his scheme and confront him, he tries to hide the remaining Chemical X by swallowing it... and turns into a giant monster.
Mojo became one giant ape in the Powerpuff Girls movie. Him also did this in the episode Speed Demon and Power Noia, though into two different forms. It actually works very well for HIM in Speed Demon and for Mojo in The Movie. So does Sedusa when she tricks the Gangrene Gang into stealing three Egyptian artifacts for her. Not only does it restore her hair, it turns her into a giant, real-snake haired monster bent on destroying the Powerpuffs and Townsville. Remember, it's always about the tiara!
On the Osmosis Jones series, a corrupt mayoral candidate who has been illegally using growth hormones to sabotage his rival's campaign gets caught red-handed with the stuff, downs it in a panic, and you can guess the rest.
Kevin 11 from Ben 10 is an odd spin on this: His true form is his first form, an orphaned eleven-year-old boy with the power to absorb energy. Attempting to absorb the Omnitrix's energy, however, resulted in him losing the only thing he had left... His humanity.
Then again, there's more than one way to look at the phrase "true form":
Kevin: It's payback time for turning me into a freak!
Ben: You always were a freak, Kev. It's just that now the ugly's also on the outside.
Fortunately for Kevin, Ben 10: Alien Force ends with the Omnitrix destroyed (which Ben replaces with the Ultimatrix) and Kevin regaining his humanity as a result.
In Ben 10: Ultimate Alien, Kevin absorbs the power of the Ultimatrix to stop an incredibly powerful villain, attaining a new one-winged angel form.
Doctor Victor, from the third season finale, is another straight example, an absurdly large NASA scientist at first appearance but secretly a hulking Frankenstein's Monster-esque alien beneath the fašade.
The third season finale of Ben 10: Alien Force sees it happening a few times, with Albedo's Ultimatrix being able to unleash the "ultimate evolution" of the various alien forms. Ultimate Humongasaur is green and much stronger than the normal version, while Ultimate Swampfire is a tree with blue growths. And then once Vilgax's ship floods he unveils "his true form" - a giant squid/octopus.
Hexxus, the spirit of destruction in FernGully, has three different monstrous forms. He starts out as a wad of toxic waste, turns into a cloud of poisonous gas, and finally appears as a burnt-looking skeleton covered in a cloak of pestilence.
Characters, particularly Batman villains, in the DCAU like this trope a lot as well:
Clayface... it's easier to say he really liked to turn into horrifying things during combat;
One of the more way-out examples is the episode "Home and Garden", where Poison Ivy created a race of plant people who start out as normal-looking babies (save for the fact that they've emerged from giant seed pods) but may suddenly mutate into huge, green, ogrish thugs;
Eventually it got to the point where the Preserver assumed a monstrous form to fight Lobo in the Superman: The Animated Series episode "The Main Man".
It was even nastily subverted by the time the Batman Beyond episode "Splicers" came along. The evil scientist leader of the Splicers pumps himself full of LEGO Genetics Juice, transforming into a fearsome monster combining the features of many creatures. Terry fights him normally for a bit, then gets the bright idea to inject more of the serum into the baddie, horribly mutating him into a blobby thing... that is actually still quite capable of fighting and, worse yet, is even more powerful than before.
Speaking of Batman Beyond, the writers liked this trope enough to play it fairly straight in every other episode. The episode "Curse Of The Cobra" is a good example; as a matter of fact it used LEGO Genetics as well.
This is also the series where the writers admitted they would blow up the building if they couldn't figure out a good way to end an episode.
In the terrible trio episode of The Batman, The Trio uses skin patches to administer the Langstrom serum. In the end Fox (a guy turned anthro fox) ends up turning into a griffin-like monster.
In Biker Mice from Mars, Fred The Mutant, Karbunkle's sidekick/assistant, is mixed up of different parts and absolutely loves pain. Another episode had a villain called Evil Eye Weevil, a skeleton like thing who is a No Celebrities Were Harmed parody of Elvis and Evel Knievel. Evil Eye Weevil could shoot a "hostility beam" at anyone and anyone hit by it would start fighting like crazy. Then again, the Plutarkians were never the picture of beauty either.
In the 2006 revival, Stoker (the Biker Mice's mentor) turns into an insane rat-like monstrosity called "Stoker Rat" by the light of the sun due to radiation.
Parodied in an episode of Catscratch. While the brothers are watching a scary monster movie, they are interrupted by Human Kimberly at their door with a gift of broccoli. Gordon is fiercely allergic to the broccoli and he puffs up so bad that he looks just like the monster in the movie. Mr. Blik and Waffle think he is the monster from the movie and run for their lives. When they can no longer run they are faced with their only option: fight the beast.
It also subverted in the episode with the Banshee. The true form of the Banshee is revealed to be a "beautiful" seal woman - depicted as a seal with a dress and long blonde hair.
Happens a lot in Jackie Chan Adventures. This happens to anyone who wears one of the oni masks, and in the final season it happens to the villain Drago, or anyone else, who absorbs a demon power. When Drago gets all the demon powers, the end result is quite...monsterous. Most people would probably say that Ultimate Power is not worth the price of looking so ugly.
Captain Simian and the Space Monkeys has "Gormungus", an alter-ego of Gentle Giant Gor. For roughly the first third of the series, pushing Gor's Berserk Button sends him into an Unstoppable Rage. After the malevolent alien Apax captures Gor and decides that the temper and strength make him the perfect gladiator, but that gentle side just has to go, he zaps Gor with a home-made mutagenic raygun. As a result, whenever Gor gets angry, he grows into a massive, more feral-looking gorilla creature, sort of a cross between The Incredible Hulk and King Kong, until he gets calmed down.
And the Trix, in Season 2 (the Negatrix), Season 5 (their Dark Sirenix forms, which was a physical mutation instead of their usual costume change upgrades), and Magical Adventure (when the Ancestral Witches possess them).
Tritannus, the main villain of Season 5, invokes this in the second episode of the season when he absorbs magically corrupted oil that gives him incredible magical power. Not only has he stuck around since then, but the One-Winged Angel form is what he's used for most of the season; he's pretty much useless when in his original body, though he typically has someone to protect him when that happens. His plan seems to be acquiring another such form, which cannot be good.
Aa'une went from glowing Evil Overlord to a giant monster with several tentacles when exposed to the energies of Lake Blakeer. Then in the next episode he goes down right Eldritch Abomination by growing extra mouths and more tentacles.
Promptly subverted when Iparu's shapeshifting power allows him to assume an identical form and match Aa'une blow-for-blow in his powered-up state.
Phineas and Ferb makes a joke about this trope in the episode "Nerds of a Feather". A TV producer Dr. Doofenshmirtz has captured to pitch a TV idea to, who is voiced by Seth MacFarlane, says that when the holographic monster that Phineas and Ferb have made comes out that "having monsters come out of no where at the end of stories is lazy story writing."
A human example with Silas in Transformers Prime. After being mortally injured when Nemesis Prime falls on top of him, his mind is transferred into the body of the recently killed Breakdown.
Venger, from Dungeons & Dragons, transforms into a monster in the episode "The Girl Who Dreamed Tomorrow".
In the Foster's Home for Imaginary FriendsMovieDestination Imagination, Mr. Herriman makes the mistake of verbally threatening an emotionally unstable Reality Warper named World with the thing he fears most, to be sealed away alone again. World replies by destorying his imaginary world and transforming into a massive chimera creature to try and reclaim Frankie, the only person in years who has treated him with kindness. It actually works out pretty well for him as no one can really stop him until Frankie calms the poor kid down.
There is also Atomic Betty villain Maximus IQ becoming a giant demonic cat when he wore the Amulet of Shangra-La-Di-Dah in its titled episode.
My Little Pony 'n Friends: Lavan, villain of the "Quest of the Princess Ponies" serial, transforms to a powerful crystalline form by absorbing the magic of the six great Magic Wands he stole from said Princess Ponies. His careless wresting of the power from the wands disrupts all the world's magic, meaning that doom is coming on two fronts.
Thundercats: "Ancient spirits of evil, transform this decayed form into MUMM-RA, THE EVER-LIVING!!" Snarf proves that anyone can channel the 'ancient spirits of evil' if they're allowed into the transformation chamber. This might seem disloyal of them, but hey, the spirits are evil...
Aaahh!!! Real Monsters featured Ickis, a small red monster with an unfortunate resemblance to a bunny rabbit. He also comes from a long line of loomers, meaning he can size shift into a gigantic beast with red eyes and dripping fangs. For the humans he managed to scare, he definitely came across a One-Winged Angel.