Played with on Adventure Time. Jake is a magical shapeshifting orange dog, but he DOES wear nearly invisible pants woven by pixies.
In American Dragon Jake Long, when Jake transforms into his dragon form his clothes disappear, same goes for the other dragons. When he transforms back into human form his clothes reappear. This is lampshaded beautifully by Jake's dad in the last episode:
In Avatar: The Last Airbender , during the climactic duel, Aang and Ozai end up wearing nothing but their trousers, which seem to be fireproof (possibly justified given that they're in the Fire Nation at the time).
In Batman: The Animated Series, the episode featuring the return of the Man-Bat (a person who was effectively a werebat) has in addition to a Magic Pants, a Magic Shirt. Rather than being the prime suspect, it's his wife, and though her transformation shreds quite a bit of her shirt, it's still enough to keep her decent when she turns back. Except for the earlier times when the Man-Bat had no shirt at all, but we never got to see the times when she turned back then.
Batman: The Brave and the Bold seems rather confused about how Blue Beetle's armor works with his clothes—sometimes he has to take off his shirt before activating it (since the armor comes from his back), sometimes he can do it fine fully-clothed. And when he comes out of his armor, he may be dressed normally or in his boxers, regardless of what he had on originally.
In Ben 10, Ben's clothes are outright said to be a memory of what he was wearing when he booted up, so they're incorporated into what the alien form is wearing when he transforms. When the alien isn't wearing clothes, then they just sorta disappear most of the time, though in a few cases, most notably Cannonbolt, they look like they're incorporated into the alien's skin. Good thing, as he only has one outfit.
And in the What If? episode "Gwen 10", where Gwen gets the Omnitrix. When Gwen accesses an alien form with clothing, the outfit is blue to match her shirt instead of Ben's white-with-black.
Gandhi in Clone High shrinks in a "trippy adventure through his subconscious" and happily notes that his clothes shrink and his voice raises in pitch miraculously in proportion with his body.
In an episode of Codename: Kids Next Door all the weredogs have magic clothes that appear as they change back even though they ripped off as they were changing into weredogs.
Averted and played straight in Dexter's Laboratory, to ridiculous extents. Dee Dee eats one of Dexter's experiment cookies while donning a rat costume, and her costume turns to shreds when she becomes huge. Somehow, her normal clothes stay intact as she transforms into a 50ft giantess.
Used almost literally in Fairly OddParents, where Juandissimo will flex, ripping off his shirt and showing off his muscles...and then uses magic to poof another shirt onto his body. Sometimes he goes through several shirts all at once just by holding his pose.
Spoofed in Futurama. When Leela tells her parents she is Clobberella, she rips off her usual outfit of tank top, pants and heavy boots to reveal a sleeveless, leg-baring superheroine costume beneath. A few moments later, she rips this off too, revealing...another tank top, pants and boots. (Her explanation: "It was brisk. I dressed in layers.") Extra-absurd because the original tank top wouldn't have covered the shoulder pads from her costume, her costume had bare legs that wouldn't have covered a hidden pair of pants, and her long pair of gloves simply appeared and vanished at a whim.
Also handwaved in the episode "A Bicyclops Built For Two": Leela meets the the only other cyclops — Alkazar — who turns out to be a shape-shifter using the "I'm the only other member of your species" tack on four other last-of-their-kind females. When asked why he made the foolish mistake of trying to marry all of them at the same day he points out that a tuxedo that shifts shape with its wearer is very expensive to rent.
In Gargoyles, when a gargoyle turns to stone during the day, any personal possessions he has on him (including clothing) will turn to stone with him. Word of God says A Wizard Did It in Roman times with a "spell of humility", and that there's a story there to tell (if the series would stop getting Screwed by the Network long enough to actually tell it).
Averted with Fox in Eye Of The Beholder. When she turns back she's completely naked, and Elisa, whose wearing a Halloween costume over her normal clothes, takes the skirt off so Xanatos can cover her up.
Surprisingly averted in the pilot of Generator Rex. When Rex cures a man who has mutated into a skyscraper-sized monster, the man is naked when he reverts to normal. Apparently this is common enough that the goon squad following Rex had a towel on hand in anticipation. It's played straight in later episodes, as most Evos revert to fully-clothed humans, or at most have a ripped shirt. This would seem to suggest that the poor bastard in the pilot was already naked when he turned.
Justice League occasionally dips into this, but the most egregious example occurs in the episode "Double Date", when Villainous Glutton Mandragora charges at Black Canary and she hits him point blank with her Canary Shriek for about 10 seconds. His shirt, naturally, is completely incinerated, since the attack should be fatal at that range, but (luckily) his pants are fine. And oddly enough, his shoes don't survive the attack, suggesting that they're literal magic pants.
Averted after Flash defeats the Luthor-Brainiac merger. Luthor's very clearly naked for the rest of the scene afterward. Granted, Luthor wasn't wearing pants in the first place, but it's still surprising they had him outright naked even if nothing was shown.
The villainess Giganta's outfit always fits when growing to giant size. Anything she's wearing seems to grow at the same pace she does. However, as Shade learned to his delight, keeping the same relative size does nothing to prevent people from looking up.
The "Grande Size Me" episode in the fourth season of Kim Possible, aside from being an Anvilicious episode espousing healthy food choices, also had Ron turn into an enormous, yellowish, Incredible Hulk-like thing that talked in Hulk Speak and craved fast food. When he turned back, they oddly went with the Running Gag and had him reduced to his boxers—which were intact.
"ARG! RON Lose pants..."
Not to mention the episode where he transformed into a large, naked, mutant beaver, and when he got better his clothes spontaneously regenerated.
And then there was the time Ron put on the muscle enhancing ring and suddenly got all buff...his clothing survived the transformation perfectly intact. This seems to be a hidden theme with Ron.
Sort of played straight and sort of not in the episode that introduced DNAmy. She combined Mr. Barkin and Rufus into a naked but not particularly childhood-scarring monster. When the two were separated again, Rufus was wearing a miniaturized version of Mr. Barkin's original outfit, and Mr. Barkin was urgently requesting pants.
In one episode of Phineas and Ferb Doof invents the de-evolution-inator to de-evolve everyone to take over the Tri-State Area. The ray from said Inator hits Doof until he is a single cell organism. When Doofenshirtz uses the Inator to evolve back to human, he finds interesting that his socks and underpants evolved with him.
In an episode of Robotboy, Tommy tries to drink a potion that he knows will turn him into a savage giant, because that's the only way to save Robotboy. However, the potion slips out of his hand, and Lola catches it. Knowing that they're running out of time, Lola drinks it instead. Even though she immediately grows nearly twenty times her original size, her dress never even gets as much as a single shred.
Some characters in The Secret World of Alex Mack are given the ability to transform/affect anything in physical contact with them as well, including their clothes.
In the pilot, Alex Mack didn't have this ability (although only on her accidental first try), but obviously they couldn't get away with having their (underage) heroine end up naked every few minutes, could they?
Spoofed in The Simpsons in the episode, "I Am Furious Yellow". Through a series of pranks by Bart, Homer winds up covered in green paint and shirtless, throwing him into a whirlwind of rage. What's Bart's only reply after beholding the sight he's put into motion?
Bart: Thank God his pants stayed on.
In the Simpsons comic book, Homer once ended up becoming 50 ft tall as a result of an experiment performed on him by Mr Burns. Most of his clothes are destroyed in the transformation, including his pants.
Marge: Thank goodness for Super-Stretch underwear.
Played straight with Mark Allan/Molten Man—activating his powers dissolves his clothes, but for some reason he still has on a pair of shorts. When he first turns back, his pants are suddenly normal too.
In the BBC Wales cartoon SuperTed, the eponymous teddy bear would transform by unzipping his skin revealing his costume beneath. He was also seen to transform back by the same method with his skin underneath the costume. This led to a certain amount of horror; one could imagine his body gradually shrinking to microscopic size while still attached to a normal sized head.
Averted in the 13th episode of Symbionic Titan when Ilana is turned into a monster by a virus implanted from a reptilian beast her clothes are shredded bit by bit, when she changes back she's naked Lance quickly gives her his sweater to cover her up.
This is taken even further in Team Umizoomi. They're waterproof and and can change into different outfits.
The question of what exactly happens to Beast Boy's uniform on Teen Titans whenever he changes into an animal is never explained, or even attempted to be explained. In an episode where he is infected with a virus that turns him into a werebeast his clothes are shredded — in fact the second time he transforms into the monster he completely tears off his clothes (pants included) and yet when he changes back his pants are intact. In the comics, Beast Boy's outfit was some sort of unstable molecule suit similar to the Fantastic Four outfits. The thing would basically break apart and float on his skin, then reassemble when he scaled back to human form.
Raven's uniform seems to be able to not only change in size as needed (larger in Nevermore, smaller in The End), but can also change between the normal black/blue and white based on her father's influence over her or her mood (in Spellbound when she falls in love, in The End bringing her father to earth strips her of most of her memories and powers).
Carter in the 1987 Teenage Mutant Ninja Turtles series always has his clothes intact when reverting to normal after his mutated transformation. Averted the first time he transforms, but played straight on all subsequent occasions.
Merrily played with in 'The Tick vs. Dinosaur Neil'. As the titular Dinosaur Neil, grown huge and apparently nude, rampages through the city, the mad scientist character who appears occasionally has somehow already built a pair of appropriately-sized pants. The pants (held up by something that looks sort of like a shuttle gantry) are promptly struck by lightning, and Dinosaur Neil is subdued by other means, shrunken back to human... where he is once again wearing his dinosaur costume. I'm not sure if this counts as a subversion, an inversion, an aversion, or what...
Scientist: Bring him to zhe pants...
In Ultimate Spider-ManAlex transforms into the Rhino with his clothes just vanishing, only to reappear when he returns to normal. The angles chosen for his transformation scenes seem designed to keep the audience from seeing how this happens.
Beast Boy also appears in Young Justice, where his costume seems to shrink into a collar whenever he transforms. Becomes Fridge Brilliance when you remember that his "blood sister" Miss Martian, another shapeshifter, has special clothes that adjust with her—she probably just got him some of those.