I have several spares boxes.
4 boxes for decals (Modern, U.S. WW2, German, and everything else)
Parts are also organized by...small parts(stuff useful for cockpits, gear bays etc)...ordnance/stores...figs....clear...wheels...and a big, non OCD, clutter box for just about everything else.
I used to save every box along with it's spare parts and inst. sheet. I'm over that! That was fine when I only had 15-20 builds...now, with close to 1000 under my belt...NO WAY! Aside from any remaining useful parts, everything goes in the trash, without sentiment.