I'm surprised no one's mentioned using comic book boards to organize smaller pieces of fabric, less than 2 yards... Fold your fabric with selvedges together, then fold that width in half again, and you will end up with just the right size to wrap around the boards and make "mini bolts" of fabric. I recently bought a bookcase to store all my mini bolts on, like books on a shelf. It makes it so much easier to see everything, organized by color.
For the longer length pieces, I wrap them around my long cutting ruler then pull the ruler out. I stack those folded pieces horizontally, like a stack of full-sized bolts. I love being able to see all my fabrics now!