I save my boxes, too. I have some of the leftovers in some of them (instructions, decals, etc), but eventually I sort everything out, sprue into a sprue bin (I save it for Anthony Fuentes-captfue at Agape and elsewhere. He uses sprues as his raw material for sculpting), instructions and decals into binders, and spares in the spares storage. The boxes I would like eventually to frame; seems that the lids can be flattened easily enough and tucked into some poster frames.
I wish I had the boxes from when I was a kid, but many of those, I cut up, to make posters from the box art, and the rest I chucked when I went off to college. Wish I still had those...