I sort mine by color, but also by size. All the large 2+ yards are together and then I have Sterlite storage drawers that hold all my small stuff. I use the little boards to wrap it on and then into the drawers...I do a lot of donation quilts so I use them up for that or my applique quilts.

I sort mine by color -- then put the odd balls in a separate stack. I generally use the background color if it is a print.