I predominantly work and store by color. I have the plastic coated wire cubes in a closet and one color is in each cube. The largest pieces are on the bottom and the smaller on top (approximately
). Fabrics that are hand dyed, hand painted, 30's, batiks or Asian are stacked separately on a shelf. Fabric selected for specific projects are kept together. I've tried many different sorting systems and this is the best one so far. It's been the same way for 10 years now.
It seems we each have to figure out the system that works best for us.