Congratulations on your 'she cave'. I also took over my sons room when he moved out. LOL
I sort my stash in wire baskets, hubby bought them from Lowes, instaled them in the closet.
I sort by color, a separate basket for crib/childrens prints. All my solids in another bin.
When I purchase fabric for a specific quilt I keep this fabric in its own stack with the pattern on top. Then when I'm ready to start this quilt top, all the fabric is in one place, keeping the fabric from accidentally being used in another quilt.. Every one organizes their stash differently.
Just keep in mind you want the fabric away from sunlight, and do not store fabric in plastic bins, fabric needs to breath.
Have fun, when organizing you get to see all your beautiful fabric. :0)