When I finish a kit that has leftover parts I transfer them, along with the direction sheet, into a gallon (or quart) sized ziplock bag. I cut the end flap from the box and put that in the bag as well. I then keep the bags together in clear "under bed" totes. You know, the kind that are somewhat shallow but large width and lengthwise. I label the totes by year, or theme, of the kits. Any leftover tires and decals are the only thing I keep separate from the kits. For me, I find it easier to keep the parts like this rather than cutting them free from their sprues and trying to decide how to classify them to keep them with other like parts. It really doesn't take me too long to find kitbashing parts from these totes, but granted I only have maybe 30 or so leftover kits to go through.