I have been organizing my scrap piles into colors for some months now and I finally had a chance to stop and do it all at once on 11/24. Close to being finished I ran out of the plastic shoe boxes (of course) to store them as I had been working up until 11:00 pm, I told myself to just put them color sorted into plastic baggies and purchase the containers the next day. That way it is sorted and you are that much further along in the process.
This is what my scrap pile looked like before (there are more bins next to it and stuff was in baggies):
This was my attempt to sort them by size, that got old real quick.
Here is what it looks like now, still needs more work, but it is much better than before. I find it alot easier to use the bins this way because if I need a certain color, I start there before I go into my actual fabric stash to cut a size that is not in the bins.