I'm working on this very topic in my head right now. I've got three quilts going so can't reorganize fabric yet, but soon. Since I've gotten into making scrappy quilts from Bonnie Hunter's books and website, I am rethinking my fabric storage. I do have large pieces (FQ's and half-yard pieces) that I have sorted by color, others by theme (patriotic, Christmas, etc.), too. Recently, though, I've been cutting a lot of scrap pieces and strips and sorting them by size (1.5", 2", 2.5", 3", 3.5", 4", and 5"). I have a tall 10-drawer plastic "cart" I used in the classroom into which I am now putting scraps and strips as I cut them. I've two "Leaders and Enders" quilts in mind and am collecting pieces for them.
Since the drawer cart is pretty flimsy and doesn't work very well and since the casters on my cutting table have broken, I have asked my DH to make me a new table. He's really, really good at woodworking and furniture building! I've decided to have him built two columns of shallow drawers on each side into which I can put my scraps and strips by size and leave an open area between them for batting and a couple of large plastic tubs into which I put scraps for animal beds and current projects. It's taken me a few years and the making of a variety of types of quilts to finally arrive at a solution for me. It may or not work for anyone else. I suspect everyone has his or her own solution, with some commonalities.