I have different sized plastic drawer modules for different sizes of fabric--then sorted by color. I use the plastic shoeboxes for fat quarter sized fabrics. I use smaller three-drawer units for tiny pieces (good for paper piecing). Then I use the larger three-drawer units for yardage. Works for me, and I like that I can see through the boxes so that I know what's in a drawer without opening.
Also, I keep separate bins for works in progress or projects I'm going to start soon.