Hey what about the outer shipping boxes? Are they worth saving in addition to the item's shelf box? I am unpacking all my trains to store on train room shelves. The brown cardboard shipping boxes take up a lot of room and I'd rather not keep them. None of them are older than 1995 anyway.
If you actually keep the inner boxes inside the shipping boxes, it's not a lot of extra room. (well, it adds up a little based on the thickness of the cardboard, but I assume you mean keeping them separate form the inner box?)
They can help protect the inner box so it doesn't get as much shelf wear over the years (dinged corners, marks from sliding across the shelf, etc).
Value probably not a huge differential, but they definitely can help preserve the inner box. Given a choice, I prefer an item with the shipper, assuming it came with one.