I keep all my crumbs, for me 1" and smaller, together in a recycled clear plastic salad container. When it is full, I stuff it in an envelop and send it off to someone on the board who likes to do crumb quilting.
I keep all my dimensional (squares, rectangles, strips, etc) scraps in a plastic drawer together, well, 2 drawers now. I keep the rest, odd shapes and sizes, in plastic shoe boxes sorted by color. My inclination now is to sort the dimensional pieces by color also, I just have to figure out how to store it all as it won't fit into the shoe boxes if I put them all together. The way I have it now is really not convenient if I want only one or two colors in the dimensional scraps as they are all mixed together.
Even tho I am a mainly scrappy quilter, I do seem to be tending towards doing controlled scrappys. That makes sorting by color seem more useful for me.