If you sort by "usable in crafting," the ID card and the book don't belong.
If you sort by "edible," shells, wrapping paper, obsidian bits, and kat hat mats, mask fragments, and gremlonium and such don't belong.
I don't test which valuable materials I can waste very often, so I might be mistaken slightly on what's edible or not, but I know that the ones from Mt. Krampus and Shadow Lairs aren't, and hope the others aren't.
The ID card is crafted but not used in further crafting.
Frankly I'm a bit surprised it's not considered a Key.
Turning them into tokens would also make it impossible to trade them which would kind of suck if you, like me, constantly have 15 extra of two kinds of tokens and none of two other kinds.
The Glyphs found from fiends should stay as mats. However, I do agree with Addy that the ID Cards should be keys. It makes sense, since it unlocks the gate to the Torto fight. It would function the same as the Shadow Lair key.
Problem?