Whenever Astro Boy gets in a fight all his clothes usually end up getting shredded aside from his iconic belt, briefs and red boots. Note that this doesn't apply to the original manga where these were explicitly part of his body, whereas in later versions he is said to be designed to emulate humans perfectly.
In Black Blood Brothers, when the "Old Blood" vampire Cain Warlock transforms into his blue wolf form, his clothes are torn to shreds and he triples in size, but those trousers remain unscathed.
Averted in Claymore: the organization's ultimate weapon, Alicia, who transforms in a slightly-more-than-human sized creature with blades for arms, has a special uniform made of a material that apparently stretches to accommodate her changed form. How the hell it doesn't tear or dull the blades is, however, not explained.
Helen is said to have similar material for the arms and legs of her uniform, since she can stretch her arms and legs to great lengths.
Another character with similar transformation powers is seen disrobing before engaging in battle so that her transformation won't ruin her dress.
Totally averted in Devilman Lady, where Jun destroys her garments every time she transforms into a muscular she-devil. Her handler Asuka remarks she needs to remember to bring extra clothes for her after missions.
Allen Walker, the protagonist of D.Gray-Man, has a left arm made of Innocence. When he activates it, it becomes a huge, armored claw that goes all the way up to his shoulder, even though he usually wears long sleeves. Lampshaded in one of the manga volumes, where he answers a reader's question about it.
Allen: I have no idea. I'm just glad it doesn't rip.
In Digimon Frontier, the Transformation Sequence involves clothes shredding, the better to facilitate a Sailor Moon-esque naked transformation. Clothes are always returned upon demorphing. Explained by the fact that in the Digital World, your appearance is based on your picture of yourself. That's why, in other seasons, the Digidestined's clothes automatically changed when they entered the Digital World no matter what they were wearing before.
In Digimon Tamers the final evolution's Transformation Sequence - Biomerge Evolution - does not show what happens to the human partners' clothing during the process. Perhaps this has the same explanation as "Digimon have no gender" being the reason that the human partner has no naughty bits during the sequence - Digimon also technically don't wear "clothes".
This trope is inconsistent, but present, in the Dragon Ball anime series.
When the saiyans transform into Giant Apes, they are naked when they change back to normal. In Dragon Ball Z, Freiza's army, including the Saiyans, wore special armor that was literally one size fits all. Even when Vegeta transforms into a Giant Ape inside them, they still fit. Bulma later replicates this armor.
This is pushed a bit far in the Bardock special, characters that are clearly wearing cloth material in addition to their spandex or whatever bodysuits still have it on them in Oozaru form, but despite being stretched out so much, it still wears as loosely as it did on their normal sized form.
In Dragon Ball GT, Goku's Super Saiyan 4 state always has his pants in a good condition, despite the fact that Goku has a child body with child clothes and the transformation makes him grow into an adult. The first time Goku reached the state, his clothes were previously destroyed because he had turned into a giant ape... and the pants reappeared anyway. Vegeta keeps the same pair of pants he was wearing when he makes the SSJ4 transformation. The pants are apparently just a part of the transformation, which would seem ridiculous if using ki for a wardrobe change hadn't been in place since the first season of Z, if not before.
In Dragon Ball, Goku even lampshades this in first fight against Piccolo Jr. when the latter grew to gigantic proportions, with Goku asking how his pants grew with him.
Kenshiro from Fist of the North Star has a tendency to "hulk out" when facing foes he particularly despises or has difficulty defeating, destroying his jacket and undershirt in the process. He seems to have an infinite supply of these jackets and undershirts, as they are always replaced without explanation by the beginning of the next episode — and sometimes, by the beginning of the next scene. Justified in that he quite literally absorbs it and re-extrudes it when he's finished.
Averted in Fruits Basket; the characters transform back from their animal forms au naturel. The exception being when Kyo transforms into the super-ultra cursed version of the cat, and gets a pair of his very own magic pants even when in the form of a...lizard-cat-thing. Justified in that the size difference was small enough that they simply stayed on, rather than fall off as they do in most other cases.
In Fullmetal Alchemist, Major Armstrong's shirt tends to explode with alarming regularity and he is seen shirtless for several scenes after he rips his shirt (and the gag/fight is over). His pants are far more durable.
In the anime, Edward Elric is constantly doing that to his trademark coat and, sometimes, even his shirt. And he doesn't take it off, he rips it off, as seen in the first chapter. He can make new ones with alchemy.
Averted in the case of Naraku, whose outfits tear when he transforms in them. At one time, he is clearly shown to be unclothed after Sesshomaru cut him to bits - He regenerated, his outfit obviously didn't. He tends to carry a more transformation-friendly, loose-fitting baboon pelt robe with him to cover himself afterwards.
In the "pants are indestructible" vein, whenever Inuyasha transforms into his full demon mode, usually his shirt has already been shredded in the process of gaining a life-threatening injury or will be completely destroyed in the ensuing battle - but his pants remain untouched, never even getting a bit ragged around the edges. Incidentally, he also regains his shirt (fully intact) after every battle with no explanation as to how it got there/was repaired.
Tsuna from Katekyo Hitman Reborn! burns off all of his clothes save his boxers every time he gets hit with the Dying Will Bullet. Why only his boxers aren't burned off remains a mystery...
In Kemonozume, the Flesh Eaters usually keep just enough of their clothes intact when they transform, and they still fit when they revert. However, when Kazuma transforms near the end, he is left totally naked.
Magical Project S in an episode, both Sasami and Pixy Misa age to teenagers and grow and become very tall, yet their clothes remain the same. Oddly enough, when the potion's side-effects kick in and they turn into babies, Sasami's clothes look huge on her while Misa's change along with her.
Setsuna appears to go between releasing her wings by lifting the back of her shirt to having them appear directly through the cloth without tearing (possibly justified in that pactio-registered outfits can revive). Akamatsu, given the time, will occasionally illustrate her wings visibly appearing under the cloth, but falls into this when rushed (he focuses the camera at angles where the viewer can't tell).
Kotaro tends toward this as he transforms into his beast form (pants perfectly intact).
When the cast use age-changing pills, their clothes do not transform. When Evangeline aged back to her younger form on Negi's "date" during the Mahora Fair she had to adjust her dress to fit. When Konoka aged up to 20 her pants needed to be unbuttoned and her shirt was skin tight, when Chisame aged down her pants (and panties) fell off under her shirt (which was now as long as a dress). Negi and Kotaro are never shown aging up, but they change their clothes when they do. Making this a subversion, except... For whatever reason Chachamaru's robotic ears change style to her younger models from the Mahora Fair arc. However Akamatsu's Word of God says we shouldn't think about this too much, the age pills are magic that work on robots.
Then there's Takane, who, tired of Clothing Damage, starts wearing literal magic clothes that double as armour. However, they have the glaring flaw of having No Ontological Inertia (as she experienced by fainting after a fight with Negi), and are of little use against Asuna... proving that in some cases, regular pants are superior.
In the second season of Magic Knight Rayearth, the trio discuss what happens to Fuu's glasses whenever they transform. They're not entirely certain, but the glasses always come back afterwards, and her vision isn't impaired during her transformed state.
Averted in Moldiver, where in the heat of the moment Mirai sometimes forgets that her Transformation Sequence destroys clothing and finds herself naked after transforming back if she doesn't remove her clothes and fold them tidily away before activating the Mol unit.
Averted by the second stage of the Cursed Seals: Tayuya growing horns ripped up her hat, Kimimaro growing spikes out of his body and a tail destroyed his shirt and ripped a hole in the back of his pants (and he pulled down his shirt when growing bone weapons out of his body or ripped holes in it), and Sasuke growing wings ripped two huge holes in the back of his shirt (he starts wearing an open shirt which he can pull down easily after the Time Skip).
When Itachi was hit by Kirin for some reason his Black Cloak completely disappeared but what he was wearing under it didn't move at all.
Orochimaru (and temporarily, Sasuke) can shed his skin to regenerate, and like Pepper the clothes are treated like they were part of his body.
This becomes a plot point when Darui fights Kinkaku and Ginkaku: when Kinkaku did a tailed beast transformation which resulted in the weapon he was using being unreachable and thus eliminating the possibility of using it on himas happened to Ginkaku.
First averted, then played straight in New Grappler Baki due to an art continuity error. After Dorian gets set on fire, he inexplicably goes from being in his underwear (with his pants gone entirely) to wearing the convenient remains of his sweat pants over a couple of chapters.
In One Piece, many characters have eaten one of the fabled "Devil Fruits", which grant superhuman powers to the eater. "Zoan" Fruits grant the ability to turn into animal forms, "Paramecia" Fruits do all sorts of crazy stuff (like the main character's rubber body), and "Logia" Fruits allow the user to transform into natural elements. With the exception of one possibly non-canonical movie, one character with an age-controlling fruit and another character with rejuvenating powers, in every instance the user's clothes change size or transform in tandem with whatever powers their user has, even if they're new clothes.
The creator of the series, when asked how come when one of the characters (a woman that could extend any part of her body as a hard as metal spike) used their powers, they didn't shred their clothes in the process. He stated that if he had done it realistically, the manga would have had too much unnecessary nudity (not to be confused with necessary nudity, see below)
In one chapter, everybody becomes wax sculptures, and are freed by Usopp's flaming slingshot attack. Everybody who turned into a wax sculpture loses their shirts, (yes, including Nami and Vivi) but they keep their pants.
Jewelry Bonney seems to be an exception to this: when she uses her powers to turn some Marines into children their clothes stopped fitting and she wears loose, skimpy clothing with suspenders that fit even if she turns herself into a child.
Likewise, in One Piece Film: Z, Ain's Devil Fruit also averrts this, leaving her victims as children in oversized clothing. Nami and Chopper can attest to that.
Robin has come to rely on this a bit after the Time Skip. Before she would only use her power to temporarily create copies of her body parts on nearby surfaces to create individual parts like arms, eyes, or legs, which always remained bare. After the Time Skip, she learned how to create complete copies of herself, and also somehow gained the ability to create extra outfits with which to clothe those copies. Though this makes sense given Oda's reasoning in the entry above.
Extreme example in Pandora Hearts: When Alice turns into her Black Rabbit form, not only do her clothes change size with her, but her miniskirt turns into a pair of pants! (Could be justified by magic.)
Averted in Princess Tutu. The main character repeatedly turns from a human to a duck and back again, losing her clothes in the process and having to constantly hide somewhere to redress. However, it's played straight when Ahiru transforms into the titular Magical Girl.
Applied inconsistently throughout Ranma ½. Sometimes characters have their clothes on and intact when they transform back from their cursed state, but usually not, often causing people to realize that they turned back to humans but can't go anywhere because they're in public. The only one who always transforms back with his clothes is Genma, since presumably none of the audience wishes to see a fat middle-aged man naked.
This is especially noticeable in the case of Pantyhose Taro. All of the others transform into small animals (pig, cat, etc.) and their clothing either vanishes or crumples to the floor. However, Pantyhose Taro transforms into a multi-story bull/yeti/crane/eel/octopus chimera, and he always rips his clothes to tiny little shreds when he does yet they're always still there when he transforms back.
The people of Mt. Phoenix, when in their natural state, wear open clothes and boots that allow for their wings and talons to stretch out unimpeded. But if they transform to human, they add jackets and normal boots, which are ripped apart when they revert to their true forms. It doesn't seem to bother them.
Ranma himself deserves a mention. Unlike the others he changes genders instead of into an animal, causing his normal clothes to be too big and hang loosely when turned into his smaller girl form; it takes the space of a panel for "her" sash to tighten around her waist and for the rolled-up sleeves to adjust to her shorter arms. Conversely, almost any fitting clothes he gets put in while a girl end up streching as they are too small (but not small enough that they'll rip) if he returns to normal —the exception being a steel corset that was forced on female Ranma by a domineering governess, and which was small (and inflexible) enough that it crushed male Ranma's torso quite painfully and effectively locked him in female form for the duration of the ordeal.
Rosario + Vampire does a Lampshade Hanging on it in one of the Omake. Given that nearly everyone in the manga is some sort of monster taking on human form, Magic Pants must be part of the school dress code.
Averted somewhat in at least one scene in Capo2 of the manga where Kurumu's wings can be seen tearing through the back of her shirt as she transforms. There's no clear angle to see if her shirt has magically repaired itself after that. One panel in the first series shows that her wings have clearly ripped open the back of her shirt/sweater. She suffered further Clothing Damage during the battle so it's hard to say for sure what happened after that.
There's also at least one scene where you can see her tail pushing the top of her undies down from where it's sprouted, apparently around the base of her spine.
s-CRY-ed has a couple of takes on this. Some of the time, armor-like Alters just layer on top of clothes, but in the case of Kazuma's Shell Bullet arm, his actual arm is deconstructed and rebuilt (or just outright vaporized). When he changes back, the clothing on that arm is still there. Could be justified by the fact that they psychically rearrange matter to accomplish these feats and just instinctively know how to put things back together.
Averted with the gold dragon Filia Ul Copt in Slayers. While she does seem to produce a new outfit every time afterward, she explicitly states that the old one gets destroyed during the transformation from human to dragon. This comes into play when she is locked up in a cell and mentions that she could simply change into her dragon form to escape, but would end up naked during the transformation and politely asks the guard to turn his head. The guard refuses. Not because she was trying to escape, but because he didn't want to miss a chance to see her naked.
Averted in Spice and Wolf: When Horo has to transform into a Canis Major to resolve a crisis, her expensive clothes are torn to shreds. To avoid having to buy an another set of clothes, she disrobes first when she has to transform again.
Tokyo Mew Mew, aside from the whole Magic from Technology thing (being injected with Red Data Animal DNA actually turns one into a Magical Girlwith all consequences), includes two characters whose cat genes cause them to turn into actual cats. When they regain their human forms, their clothes are intact. Furthermore, in the cat form, one of them winds up wearing an item not present in their regular costume at all.
The main character of Ultimate Girls, Silk, learns the hard way that this trope does not apply to her universe the first time she transforms into a 100 foot tall warrior justice and is naked upon reversion because her clothes were shredded in the magical girl style transformation. She and her fellow Ultimate Girls must from then on make a point of stripping prior to transforming.
Pepper of Urusei Yatsura has the power to shed all of her skin at will. Her clothes are treated as if they were part of her skin, as when she uses the power both her and the shed skin are fully clothed.
The anime version of The Violinist of Hamelin is particularly egregious about this, especially in the second season. Every time Hamel transforms into a demon his clothes explode off him dramatically, and they're almost always completely intact when he changes back. Made even more painfully obvious when his all-black outfit that Flute made him apparently becomes his trademark that people recognize him by in his travels. What the hell...?
Averted in the Wild Series. Whenever the characters transform back to human from beast form, they are naked. Mostly.
In Xam'd: Lost Memories, turning into a Xam'd apparently rips through your clothes, yet when you turn back, the clothes are fully intact. Somehow. The similar Humanform Weapons also seem to tear through their clothing but we never really see what happens when they turn back to human (IF they even can).