In Altered Beast, the player characters can collect a series of orbs that causes them to become more muscular and less clothed with each application, until finally taking on the form of a fully nude (yet anatomically void) monster. It's a different monster on each level, with the player characters reverting back to their original (clothed) form at the beginning of each level. Then again, you start off wearing not much more than a tunic and a loincloth anyway.
Slightly subverted in Project Altered Beast. Upon first transforming into the werewolf, all your clothes tear off; when you change back, your shirt and jacket are gone for good, yet your jeans and boots somehow return.
In the climactic battle with Titan Joker in Batman: Arkham Asylum, the Titan formula has made the Joker a huge, hulking man-thing that stands easily ten feet tall. Needless to say, his purple suit is completely destroyed by the transformation - except for a pair of ragged purple shorts.
In the Bloody Roar series of games, the transformations into the characters' beast forms explicitly tears the characters' clothing (almost always shoes, but often shirts, and sometimes their beast form is actually partially or completely naked). However, transforming back to human form also restores the torn clothing.
Averted in Castlevania: Rondo of Blood and every subsequent game that uses the Rondo sprites for the Werewolf enemy. After losing all his HP, he transforms back into a naked man and bursts into flames as per the Castlevania tradition.
Played somewhat straight in the Rondo remake on the PSP, The Dracula X Chronicles. When the Werewolf transforms back, he's now wearing a black speedo, both in the new 2.5D remake and the port of the original Rondo. The Werewolves in the port of Symphony, however, remain uncensored.
Averted with werecreatures in Dwarf Fortress: when one in human form transforms all their clothes are removed (even stuff they can still put back on, like backpacks), though not destroyed because that's not something the game engine can do yet. As a result, most werecreatures spend the majority of their time naked in human form, hiding in caves.
Dungeon Crawl used to avert this trope, as shapeshifting would unequip any equipment incompatible with the selected form, and having cursed equipment in one of those slots would make shapeshifting impossible. After people complained about how annoying this was, the developers made it so that any incompatible equipment (including cursed) instead melds into the player's body until the transformation wears off.
When werewolves return in Skyrim, so too does this trope. When the timer wears out on your werewolf form, your character reverts to your humanoid form, naked save for the magical underwear. However, all your equipment is still in your inventory and just needs to be re-equipped.
Fawkes from Fallout 3 used to wear Vault 87 overalls. He still does, but having grown into twice as tall and large as he once was, the top half has been torn, clearly inadequate to house his new physique. The lower half fits just fine.
Though it does state in one of the computer terminals that Super Mutants have no reproductive organs anyway.
In Final Fantasy VII, Vincent Valentine's Limit Break involves changing shape into a beast. His clothes simply reappear when he changes back.
Advent Children seems to suggest that the cloak itself is part of his power. Possibly a holdover from when he was first transformed, since he was wearing a labcoat at the time.
Possibly Terra Branford in Final Fantasy VI, whose innate ability, Trance (Morph in the original release) turns her into a naked, fuzzy, pink Esper, although she still wields her weapons and enjoys the stat benefits of her armor and relics. Using the command "Revert" restores her and her clothes. Might just be a case where Power Glows so brightly that it prevents anyone from seeing her clothes underneath.
And again in Final Fantasy IX, with both Zidane and Kuja, whose trance forms have all their clothes vanish in lieu of fur, yet reappear as soon as it ends.
In the Fire Emblem series, the Manaketes, Laguz, Fox Spirits, and Garou don't have any issues with their clothing, despite the fact that their dragon/animal transformations are larger then their humanoid forms, and very different in shape, as well. It simply disappears when they transform, and comes back once they revert to human form.
Averted by Panne the Taguel (and her son Yarne) in Fire Emblem Awakening; her light armor is designed to fit her body in both her humanoid and giant rabbit forms.
In Goblins Quest 3, when Blount turns into a Wolf Man, all of this clothes except his pants rip off. When he turns back, they all reappear.
In Golden SunDark Dawn, Sveta's clothing will magically expand to fit her Beast Form when it's activated, and then magically shrink back to their normal size when she reverts. No Clothing Damage is sustained in either transformation.
When Daxter is turned into an ottsel, he's left with only his gloves and goggles. Similarly, Veger loses his coat, boots, and pants, and Tess loses just her shoes. And when Daxter's Superpowered Evil Side comes out, his gloves and goggles grow while his pants are shredded from the knees down. Of course, upon returning to his cute lil' ottsel form, his pants are returned to normal.
Subverted in Killer Instinct with Sabrewulf's ending. After turning back into a human, his shirt rips more, and because he's only seen from the waist up for this final scene, one can only assume what's down there, or more so, what isn't.
Exaggerated in the SNES port, in which a pair of tattered shorts appears on him when he becomes human.
Link from The Legend of Zelda: Ocarina of Time. When he's a kid he has no tights. When he wakes up in the Temple of Time... tights. Magically. (Of course, he also has his ears pierced now and his hair isn't any longer than it was seven years ago, so maybe someone in the Sacred Realm gave him a makeover before sending him back)
While we're on the topic of Zelda, two words: The Legend of Zelda: Majora's Mask's Giant's Mask. Well, okay, it may be the mask that's magical and causes his clothes to grow in tandem, but it's still kind of humorous when you think about it. Also applies to the other masks.
Justified Trope in The Legend of Zelda: Twilight Princess, since the first time he transforms back to human Link's wearing entirely different clothes, provided to him by the spirits in recognition of his heroism. These clothes could very well be magical, and since the spirits already knew about the wolf thing, they could have prepared the clothes to appear and disappear in just that way. Interestingly, the wolf keeps the earrings that Link wears in his human form, which were also the only piece of clothing he had that were part of his original work clothes.
Werewolves in the game Majesty are naked while in wolf form (which is all the time when they are alive), magically gaining pants when they revert to human form after they die.
In NetHack, a self-polymorph can destroy or forcibly disrobe you of all your armor, but when you return to normal form you can sit on a cockatrice corpse without turning to stone. Hence, your character must be wearing magic pants.
Alex Mercer from [PROTOTYPE] shapeshifts constantly and never has to replace his clothes - even taking the forms of his victims dresses him in their outfits, whether they were suits, pants, skirts or body armour complete with gas mask. This is because his entire body, including his clothes, is made from superdynamic biomass that can imitate anything. On the downside, that means conventional armour does nothing except complete the disguise and his 'gas mask' will not, in fact, protect him from gas.
Averted with Rampage; when the player characters revert to human form, they cover themselves up with their hands and run off screen.
Derek Simmons in Resident Evil 6 somehow manages to change form twice, and radically - first into some four-legged predator, then into a gigantic Tyrannosaurus rex made of organs. But each time he turns back to human, his pants and boots have survived the transformation.
Then he turns into a building-sized insectoid and back, but you guess it - his pants and boots are still immune even to that.
Ragnarok (Roguelike) specifically averts this: if you polymorph into something larger than a troll, then "Your armor strains and bursts. Eight of your fingers are cut off by rings. You shall now be known as Gjarfililidan the Fire Giant."
Rune Factory 3 has characters with shapeshifting ability: Micah, Pia, and Raven. When they transform, they lose or change their clothes, but when they revert to their normal forms. their clothes magically reappear.
A variation of this trope, in Sonic Unleashed: Sonic's first transformation into the Werehog clearly shows his gloves being ripped to shreds, but when he reverts back to his original form, they magically reappear. This happens every subsequent transformation, even in the final one.
For that matter, his shoes change size and shape, even gaining spikes.
If you give your female SoulCalibur 4 character a certain piece of clothing (called spyrobe in the German version) you can clearly see that your character wears no bra. However when the opponent destroys your spyrobe you are suddenly wearing one.
Splatoon has the Inklings, who can morph between humanoid-form and squid-form freely with just the push of a button on the player's end. Only the humanoid form wears clothes and holds a gun; and what's more vexing is that when an Inkling gets splatted they leave behind their clothes and weapon, but respawn with a fresh set back at their base.
In Splatterhouse, during the fight against the mutated Jennifer, she transforms back into her human form after being hit enough times, with her clothes literally reappearing out of nowhere.
In Splatterhouse 3, whenever Rick transforms into his Super Mode, his shirt rips off, but when he reverts, his shirt grows back.
Eiji from Super Tokusatsu Wars has a transformation where he turns into a large, monstrous humanoid... completely destroying his old body in the process. Yet, if you use the Detransform action, he returns to his normal self, with the clothes he had on before he transformed.
Orin shapeshifts into her humanoid form twice in the same game, complete with dress and wheelbarrow.
Remilia sometimes changes into a bat during certain attack patterns, and if the player bombs during her final patterns, she temporarily changes into a bat too.
Mokou has a literal pair of magic pants that are immune to fire. And immune to her repeatedly dying explosively.
Similarly, fairies resurrect after being killed. One assumes this trope is in play when they resurrect, or there would be a massive clothes shortage among those with frequent dying miles like Cirno.
In World of Warcraft, Druids keep the statboosts from their gear despite not wearing anything in animal form. The gear also reappears when they transform back. Same also applies to any other class or mob with a shape-shifting ability. Notably, the Warlock's Metamorphosis (which temporarily turns the user into a demon) has Magic Pants, as does a Shaman's Ghost Wolf form.
In addition other players polymorphed by a mage, or otherwise transformed into a Sheep, Penguin, Frog or any other part of a wide ranging menagerie are also immune to unexpected nakedness, but it is magic after all.
Players can remove all their equipped gear, leaving the character naked except for a different kind of Magic Pantsnote All characters have unremovable underwear of some sort, either boxers/loincloth or a bikini.
They finally going to play it real straight in later Expansion PackCataclysm, this is going to be standard issue for all classes of playable Worgens. They can alternate between human and worgen form, but always revert to worgen when combat is initiated. Unlike druids, they do keep their clothing/armor while in worgen form (not just strangely dissappear and reappear when returning human).
The X-Men Origins: WolverineLicensed Game plays this painfully straight. Despite the game having impressive effects where Wolverine's shirt, flesh and muscles get torn up as he takes damage, this only applies to his upper body. His pants stay completely intact.
Played even more ridiculously straight if you unlock the Classic Wolverine costume, where Wolvie's regeneration suddenly now applies to the whole outfit, so as not to ruin the iconic look of the costume with clothing damage.