Sorting scraps is a constant thing. You can't just do it once and expect it to perfectly maintain itself. Unless, of course, you are awesome and put every single scrap away the second it becomes a scrap.
I will always advocate sorting by colour. It is what Amanda Jean and I encourage you to do in Sunday Morning Quilts. By far, it is the easiest method not to mention the most inspiring. We also talk about having a special category or 3 for uniquely sized pieces like strips, little snippets, or triangles.
While teaching a Values Plus class recently I, with my students, decided to try piecing based on colour as well as value. I was so excited by the results I took my scrap sorting to the next level. I took my big bag of strips and started sorting them by colour too.
The process started on the front steps, while the kids rode their bikes in the evening light. My little guy decided to stop his maniacal ride to help me. But he was so, so tired that he had to do it laying down. Hence the piles of colour radiating around him. Awesome kid.
And now I have one more section of scraps all sorted by colour. It really is a good thing.