You've opened a hot topic!!
I have a pretty big stash. Not as big as one of my friends, but that's another story. I sort by color, mostly. Solids are in one stack, hand dyes in another. I recently separated out the batiks and the Kaffe Fassetts. Then I have some small collections (i.e, cherry prints or Japanese fabrics). The rest are in stacks by color. 2 yard cuts are at the bottom of the bookcase, and humungous cuts are in another cupboard. Fat quarters and like-sized cuts are in one of those shoe storage units they sell at Target. And I do keep scraps, larger ones in one plastic box, and smaller ones in another. I read an excellent book on organizing your sewing room- the author suggested using a ruler to fold fabrics, making them all uniform size. I use an 8-1/2 inch for the larger cuts, and a 4 inch for fat quarters. It makes the room much less busy which helps me to concentrate.
I find that for me, when I can't see something it doesn't exist, so it's all visible. The room is dimly lit most of the time so I'm not worried about fading. I saw a picture of Harriet Hargrave's fabric storage area, and she uses file drawers- that wouldn't work for me since I'd forget I had the fabric!
As your stash accumulates, I would bet that you will re-organize it several times.
Kathy