I am using down my horde of fabric. How you organize depends a bit on what you make and what you have. I tend to buy a lot of novelties. Other quilters only buy novelties occasionally, if at all. Keep in mind that fabric on a shelf is subject to light damage - I've ruined some really nice fabric due to that, so now store it all in boxes with an acid free paper liner.
I have 8 boxes sorted by color (red/pink, blue, green/turquoise, yellow, white, purple, brown and black).
I have two boxes each of Asian, Thimbleberries and flannel fabric. I have 2 boxes just of backing fabrics. I also have individual boxes of Christmas/Yule, Halloween, Landscape, Ocean, and a couple of other themes.
I am gradually eliminating boxes. I'm using up the last of the children's fabric in 2 quilts, the green box is nearly empty.