Guineas plays it normal, able to turn from a normal guy into a beastly guinea pig-man form, though he prefers to stay a guinea pig being most of the time and it counts as a Reveal when his human form turns out to be handsome.
Due to the incident that produced Ellen (long story), Elliot wound up permanently able to change into the cat-man form he'd asked Tedd to zap him into afterwards in order to chase her down. Unlike most examples, though, he didn't know he could do it until he involuntarily did it again to fight Hedge. Which knocked him out.
Vlad does this in reverse. Ellen zaps him with a Gender Bender ray, turning Vlad the part bat, part bird, part terrifying monster-man into Vladia, the relatively normal girl, the only change Vlad's likely to undergo due to a Painful Transformation problem that nearly killed him the last time he tried to be human: she's not sure she'll survive a gender shift, and doesn't want to risk it now that she's finally human.
Parodied much earlier in same with "Wing-B-Gone!" Which brings up a good point: wouldn't this be really inconvenient?
Lampshaded in Golden, when the villain sorcerer decides it is times to turn into his combat form to end the protagonists, and promptly turns into... a binturong with white spots. (And not a badger at all, whatever anyone is saying, no Sir.). The protagonists even comment on this:
Sorcerer: "Enough games! With all the powers of HELL at my command, I now take the form of the Ultimate Destroyer, a [...] fiend so diabolical, so terrible, that all who lay eyes upon his visage fall into..." (his bad guy monologue drones on the background)
"...yeah, he's going to turn into a dragon, isn't he?"
"Seems rather cliché. Perhaps a giant octopus with multifarious appendages?"
One of Prof. Broadshoulders' (from Zebra Girl) defining characteristics is a "Mr. Yuk" face branded onto his forehead. Turns out it was actually a demonic third eye, and by opening it he turned himself into a demon.
Inverted in archcriminal Fructose Riboflavin's first appearance in The Inexplicable Adventures of Bob!. He first appears disguised as a handsome, muscular human, and does all his ranty monologuing in that form. It's only after his scheme has failed that he drops the disguise as pointless, revealing his mildly creepy but not very frightening wizened old alien form.
Sluggy Freelance features a random mook getting infected with a "Cheesy Bossmonster Virus", which is this trope in a tube. 
In the "Holidays Wars" story, there's one on both sides: Bun-bun becoming a quasi-god of various holidays, complete with a different colour scheme, an occasionally visible aura of power, and an updated switchblade design and fighting Santa Claus who had become an alien monster some time ago and for this fight grown even bigger. (It doesn't really make sense in context, it's just Crazy Awesome.)
It gets worsewhen Becquerel gets prototyped, though his appearance gets less ridiculous as the last prototyping's power overrides some of the previous elements. He has been shown to be able to return/retract them (at least the tentacles) with his newfound Reality Warper powers.
Lord English is essentially this to Doc Scratch, although it's not so much Scratch transforming as it is Lord English emerging from his dead body.
Possibly a straighter example with Caliborn, although English is basically a much taller and more muscular version of Caliborn, but muchmorepowerful.
Hell, the Cherubs do this as a mating action: they transform into snake-like creatures a cosmic measurement long and do battle, with the loser laying the eggs.
Oosterhuis/Ari from Panthera plays this transformation near perfectly. He even seems to win the first encounter, too.
Gunnerkrigg Court has General Ysengrin, a wolf in what is basically wooden power-armour. Normally he uses this to maintain a humanoid appearance, but when he loses his cool, the living wood turns him into something that would give Hayao Miyazaki nightmares!
In "Axe Cop Gets Married", the final boss is the alien king Cauber Helen, who's a shapeshifter and just becomes even bigger and uglier to fight. To match him, Axe Cop and his allies, some of whom were already a bit Ninja Pirate Zombie Robot, use his sons' Ultro Power to combine into what the artist (not writer) tentatively describes as "Super Hypno Double-Monkey Batman Axe Cop Familsauras Rex Wrinkles". Cauber then starts transforming into different forms, culminating in a giant sea serpent of planetary size when his opponents send another giant sea serpent against him.
White Dark Life: Most of the demon characters have either intimidating or otherwise unnerving forms they use when they get seriously pissed off. Yes, even little Priscilla. These range from Artemis, a Humanoid Abomination parodying hourglass figures, to a skull wearing thorn covered Dark Matt, and Eloria turning into a wendigo. Ironically, Altair, who is an angel, has no super powered form.
Gackt from the "Bishonen Virus" storyline of Manly Guys Doing Manly Things has two. During his fight with Commander Badass, he transforms into a gigantic, multi-winged Tetsuo-like abomination, that Commander swiftly decapitates. He then returns as an Energy Being, but at this point Commander is unbelivably sick of the whole issue and just chokes him to death with his bare hands.
Lampshaded in Grrlpower when Vehemence grows much larger and stronger.
Sydney: This had better be your final form! I have stuff to do later!