I have a very complicated organization system for my scraps.
I toss them into a bag as I go (a kitchen-sized trash bag, to be exact), where they multiply like crazy. Before you know it, there are multiple bags full. I get tired of looking at (aka tripping over) the bags, so eventually I go through and keep my favorites, and then sell or give away the rest, depending on whether the scraps are especially nice or just "meh". Last time I sold them for a few bucks at a yard sale. Then I start filling another bag. Lather, rinse, repeat.
I do occasionally go through and cut squares (usually 5" and 2-1/2"), and every once in awhile I'll make a scrappy quilt, but for the most part, the scraps just accumulate until I get tired of looking at them.