I've just started a system, so I don't know yet whether it will work. I have a couple of books on scrap quilts 'cause they're my favorites.
If the piece is about the size/shape of a fat quarter, I keep it intact for large blocks and keep these pieces separated by lights and darks.
Smaller scraps I cut into the sizes I would most commonly use: 2.5" strips; 2.5" squares; and bricks that are usually 3.5" by 5". Each of these are sorted by lights and darks.
I'm learning that the most successful scrappy quilts depend on value rather than color, which is why I keep them just by light and dark. As I use them, I can sort again into medium-light and medium-dark. Anyway, that's my current new system!
Anita