i store my fabrics in stackable plastic drawers. i can see what's inside, but they don't get dusty or faded from the light.
the drawers are fairly inexpensive and available at most discount department stores.
i try to organize by color. i usually mess up my own system when i shop my stash and so i "have to" reorganize a few times a year. i don't mind because i rediscover all sorts of things. :-)