Like Murphy I store by size. There are many containers to store the scraps. Since I make mini's from scraps, my containers are small.
Think of all the plastic containers you through out. For me it chocolate milk mix and flavored coffee containers. If I want to sort small projects by color, too, these work great. For others it may be coffee "cans", salad boxes. I purchase plastic shoe boxes (watch for sales). These work great for the larger (1.5" and above squares and strings and stack neatly.
Remember to label the container! I find using a blank sheet of address labels and a sharpie marker works fine. Happy sorting!