It sort of depends where you are at in the game, and certain habits that you have.

Among the list of things that I had way more than I could ever use:
Greydwarf eyes, bones, troll leather, trophies, beech seeds, pine cones.

Those are the sort of unwanted things that I would pick up passively in my travels. Keep two or three stacks maximum. The important thing is to keep your storage organised logically. It helps your memory out a lot when you are far away from home and trying to figure out what is most worth keeping.