In Alice in Wonderland, the title character expands to many times her own size, but her undergarments expand with her, basically becoming a minidress. Averted later when she is shrunk down and again when she grows again and is starkers.
"Who else but a clown would have an expandable sarong like this? You know, it's adjustable. I can grow to be a hundred feet tall, and I don't need a change of wardrobe. Army ingenuity!"
Averted in The Amazing Spider-Man. When Curt Connors changes into the Lizard all his clothes are ripped to shreds; only his lab coat occasionally stays on but the seams are heavily damaged. When he changes back he is very much naked.
Also averted in both the original and remake of the B-Movie Attack of the 50-Foot Woman. Naturally in the 50's original, it's not shown on camera, but in the 90's remake, it is. Also in its Rule 34 / Plot What Plot softcore parody Attack of the 60 Foot Centerfolds. (No, I'm not kidding.)
Averted in Beyond Sherwood Forest. Every time Alina transforms into a dragon, her clothes are destroyed, leaving her naked and shivering when she changes back.
Averted in Big Fish, where the circus ringmaster is stark naked after he changes from a werewolf back into a human. Even worse, said ringmaster is played by Danny DeVito.
Averted in the superhero parody Big Man Japan. The viewer might think this is going on at first, since the first time the title character is seen fighting kaiju, he's clad in purple briefs, and when he subsequently comes back down to normal size, he's wearing the same civilian clothes he was in earlier. However, later in the film, his actual Transformation Sequence is shown, and it turns out he has to undress and stand inside of a gigantic pair of purple briefs, which he then grows into.
The werewolves in Blood and Chocolate transform along with their clothes. This is just one of many things changed from the book, in which it was made a point that werewolves had to remove their clothes before changing (either because they're get ruined or because of the risk of being seen as a wolf in human's clothing).
The Cutey HoneyLive-Action Adaptation movie averts this: Honey has to wear a bra and panties, because all her other clothing is conjured up by the AI System (which runs on onigiri— rice snacks). Bizarrely, though, she has to wear a towel for her first transformation—never mind that she's dry, alone, and in her own house (although one could argue that she wasn't exactly prepared to run around town naked)
In the film Harry Potter and the Prisoner of Azkaban there is a rather stupid inversion. Animagus Peter Pettigrew at one point turns back into his rat form and his clothes come off. Problem is, every other time Animagi turn into animals and back, their clothes morph together with them. Pettigrew had in fact morphed from rat back to human earlier in the film, fully clothed, so his own transformations aren't even internally consistent.
This problem exists in the book too, but at a different point in the story. It's mentioned that when Pettigrew framed Sirius for his own murder by turning into a rat, he left behind his finger and a "heap of bloodstained robes". So if he left behind his clothes when he transformed into a rat 12 years ago, was he naked when he got turned back into a human in the Shrieking Shack?
Played straight in Hulk where the Hulk continually grows every time he transforms to the point where he is nearly the size of a small house at the end but still somehow manages to keep his pants on. However, Banner did end up naked after his second transformation, after which they give him pants that are even more magic.
This was completely averted in The Incredible Shrinking Man. Scott Carey shrinks out of his clothes and is forced to wear first kids' clothes and then doll clothes. The final scenes of the movie in the cellar, he is wearing the ragged pieces from his doll clothes because he has SHRUNK out of those.
Elvin Lincoln from Misfits of Science faced a similar problem, so usually carried a set of Ken's jogging clothes in a pocket in case he needed to shrink himself.
Lampshaded in the movie The Monster Squad, where the titular kids are having a debate on Wolfman and whether he can actually be called a "guy". One of the kids says, "What are you talking about? He walks around and wears pants..." and then the other kid explains, "He had to wear pants, see, those movies were made in the 40s. He had to wear them so we wouldn't see his...wolf dork." Later on in the movie, the kids encounter Wolfman and one of the kids "kicks him in the nards", revealing that yes, "Wolfman's got nads!"
And later, we learn that his pants are literally magic: Sean and his dad blow Wolfman to pieces with a stick of dynamite and he soon reassembles himself, pants and all.
In Pirates of the Caribbean: At World's End, when the goddess Calypso grows from human-size to gigantic, the ropes she's bound with grow with her, modestly covering her bust and her lower-than-waist naughty bits. That's right, rope also serves as magic pants!
In Space Jam, the five Nerdlucks have basketball jerseys on when transform into the Monstars and when they revert back to normal, they're buried under their oversized jerseys.
At the climax of Teenage Mutant Ninja Turtles II, the Shredder consumes an entire canister of "ooze", morphing him into the gigantic Super Shredder. His costume does not grow with him, but the fabric becomes dark and leathery, while his blades grow longer and serrated.
The Van Helsing movie takes this to a more ridiculous extreme, where every werewolf that transforms visibly shreds their clothes upon transforming, but when reverting to human, their shredded clothes are right there on their body. Even odder, part of the transformation sequence is for them to rip their previous form off of themselves like tissue paper.
Completely averted in Village of the Giants — the teens grow to enormous size rapidly and their clothing proves to be utterly inadequate. Fortunately, some giant curtains are on hand to cover their shame.
In X-Men: The Last Stand, Jean Grey (as Dark Phoenix) is disintegrating everyone and everything around her, and Wolverine gets near her. Her power disintegrates his shirt (and hischest), but not his pants. (that one was enforced by the ratings board: Hugh Jackman shot the scene wearing flesh-colored pants, but the censors requested digital pants to be added back onto Wolverine in order to keep the PG-13).
In The Wolverine, Logan's pants somehow survive being incinerated while the rest of him is burned to a crisp during the bomb shelter scene. In fact, they aren't even singed.
The Avengers is an aversion. Although The Hulk's pants grow with him as he transforms, when he goes back to being Bruce Banner he's naked. A bystander gives him clothes.