I don't have enough of a stash for a complex system.
I keep a collection together -- that's how I would remember it.
I keep all FQs together in shoebox size plastic boxes -- then arranged by color, but the repro prints stay together.
For bigger pieces, I have wire drawers, and there's not enough of them to justify a system yet!
With the scraps from a particular project that I can't bear to part with, I use the appropriate size zipper plastic bag. Usually the scraps are really small. If a piece survives that is bigger, it would go with the FQs or into the drawers.
Hope these ideas help!