I have heard that it is not a good idea to store fabric in a plastic bags - doesn't allow the fabric to breath as cotton is a natural fiber.
I store mine according to size of pieces - I know you all think I'm nuts, but I read an article in Quilt magazine (aug/sept 2009) on how to organize your stash, i.e., chunks, charms, chips, strays, strips and strings - check out the article Pg. 90. It took some time but now when I need scraps, I know what to look for! enjoy!