In the superhero RPG Aberrant, novas can take points in a background called "Attunement" which allows them to keep items on their body from being destroyed by powers like shapeshifting, growing, or self-immolation. The lower levels allow them to protect their own clothes, and the higher levels allow them to protect a whole other person. There's also Eufiber, a material produced by a nova that shifts at the wearer's will.
In Dungeons & Dragons, most shapeshifting spells and powers either explicitly have your gear change with you, have your gear meld into your body, cause your gear to fall off unharmed, or some combination of the three when you change.
At least one supplement on weres (Night Howlers for the boxed set/Rules Cyclopedia edition) not only explicitly specified that the transformation ruined clothes, but included rules for how much damage a lycanthrope would take from shapechanging while wearing (and in the process probably destroying) armor.
The magical armor enhancement "Beastskin" makes it possible for the armor to morph into armor fitted for the creature you change into and then change back with the character.
In Exalted, you'd think Lunar Exalts would go through a lot of clothing when changing shapes — especially to their massive "warforms" — but no, it just disappears into Elsewhere. On the other hand, if they're wearing Moonsilver Artifact Armour, it shifts with them no matter the form they assume — be it that of an unassuming housecat, or a bear the size of a small house. Complete with appropriately sized and shaped chainmail shirt/plate armour. No, really.
It comes back when they revert to their human true form, however.
GURPS Supers had a buyable Advantage called "Costume" — a costume that works with and adapts to the powers and form of the wearer, similar to Marvel's "unstable molecules".
In the game Werewolf: The Apocalypse, the pants very well can be magic. Although the shift from regular human to 900-pound killing machine pretty much reduces clothing to shreds, there exists a ritual called the Rite of Talisman Dedication that allows certain items, such as clothing, to become a part of the werewolf's identity. They grow and eventually turn into skin symbols as he grows larger, and return when he goes back to human. The Rite of Talisman Dedication also shows up in the game's "reboot", Werewolf: The Forsaken, as the "Rite of Dedication."
Appropriately enough for this trope, this Rite is sometimes called "the Rite of Pants" by players due to its most common use being ensuring the character isn't left naked after a few transformations.
Both games are fairly explicit on some of the nuances of the Rite - a werewolf can dedicate an entire outfit as one "object," but that only covers the clothes - not the things in them. If only, say, the pants are dedicated, then the werewolf can go around without fear of losing their wallet.
Both Mage games likewise make clear that using Life magic to shapeshift into an animal doesn't protect your clothes. Your best bets to shapeshift and keep your modesty intact are to either use Matter magic to ensure that the clothes shift to fit you, or Correspondence/Space magic to put them somewhere else.
In Vampire: The Masquerade, shapeshifting disciplines handwave this by saying the vampire blood melds clothing into the vamp's body. Or some nonsense along those lines.
That being said, if your party had a vampire sufficiently advanced in the sneaky-hidey Discipline, you could have Virtual Magic Pants For All.