In Alice in Wonderland, the title character expands many times her own size, but her undergarments expand with her, becoming a minidress. Averted later when she is shrunk down and again when she grows and is stark naked.
Bit: Vlad has a full set of clothes on when he's restored into his body. Perhaps they came with him by his shapeshifting gift.
The werewolves in Blood & Chocolate (2007) transform with their clothes. This is just one of many things that were changed from the book, in which it was made a point that werewolves had to remove their clothes before changing (either because they get ruined or because of the risk of being seen as a wolf in human clothing).
In Cat People (1942), after Irena's first transformation to and from feline form, the camera pans along tracks that change from paws to high-heeled shoes, which raises the question of exactly where her clothes go when she's a cat.
In Charlie and the Chocolate Factory, Violet's child-sized tracksuit expands along with her body when she's turned into a giant blueberry. This is quite a feat, as, in this version of the story, she swells up to roughly the size of an SUV.
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 Friday the 13th Part VI: Jason Lives, Jason Voorhees emerges from his grave as a fully clothed zombie, despite having been a rotting, maggot-infested corpse for years. In the following films, he gets dragged underwater, set ablaze, soaked in toxic waste, and even blown up, and the most damage his clothes take is being ragged and tattered. In Jason Goes to Hell: The Final Friday his body is destroyed early on, and when he eventually regenerates a new one, it even comes with his iconic goalie mask.
There is a rather stupid inversion in the film Harry Potter and the Prisoner of Azkaban. Animagus Peter Pettigrew reverts to his rat form at one point, and his clothes come off. The problem is that Animagi turn into animals and back every other time, and their clothes morph with them. Pettigrew had morphed from rat back to human earlier in the film, fully clothed, so his own transformations aren't even internally consistent.
Odd variation in The BeatlesHelp! where Paul is accidentally injected with a short-term shrinking solution — he shrinks out of his clothes and uses a gum wrapper as a Modesty Towel, then he manages to grow back completely inside his suit without as much as a skewed tie.
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.
In Justice League (2017), right after Superman is brought back to life, an explosion incinerates his shirt and shoes (he was wearing a business suit since he was buried as Clark Kent), but not his pants.
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.
In Captain America: The First Avenger, Steve's pants still fit after Erskine's serum causes him to grow 10 inches and put on 135 pounds of muscle in a few minutes. The only change is his pants are slightly shorter.
Averted in The Incredible Hulk: Every time Hulk changes back to Bruce Banner, he has to buy new stretchy pants.
The Avengers is an aversion. Although Hulk's pants grow with him as he transforms, when he returns to being Bruce Banner he's naked. A bystander gives him clothes. In Avengers: Age of Ultron, the Hulk wears special pants made from a high-tech microfiber that allows them to grow or shrink whenever he switches between his two forms.
In Thor: Ragnarok, Banner spends most of the film in some of Tony Stark's spare clothes. The pants are noted to be too tight for Banner, but they still manage to stretch with him when he transforms, lightly poking fun at the concept.
In Iron Man 3, Extremis users can heat their entire body hot enough to melt steel, but their clothes remain unburned.
Lampshaded in the movie The Monster Squad, where the titular kids are having a debate on Wolfman and whether he can be called a "guy." Patrick says, "What are you talking about? He walks around and wears pants..." Sean 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 in the movie, the kids encounter Wolfman, and Horace goes for a Groin Attack, confirming that "Wolfman's got nards!" And later, we learn that his pants are 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 can also serve as magic pants!
In Space Jam, the five Nerdlucks have basketball jerseys on when transforming into the Monstars, and when they revert back to normal, they're buried under their oversized jerseys.
Orange Nerdluck: My clothes don't fit.
Swamp Thing: When the burly Bruno drinks a chemical serum that mutates him into a hideous dwarf creature, his entire outfit inexplicably shrinks to match his new size.
At the climax of Teenage Mutant Ninja Turtles II: The Secret of the Ooze, 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 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 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. They aren't even singed.
, which raises the question of exactly where her clothes go when she's a cat.