I sort primarily by color, greens on one shelf, blues on another, some shelves have more than one color, kid's stuff together, any that are actually planned to go together (fairies) in their separate stack - put the proposed coordinating fabrics in that stack too...
Play with it a bit and see what works for you. I have modified mine several times since DS got the storage shelves put together a couple months ago. Still have quite a bit not yet sorted.