I keep my holiday fabric grouped together with the like holiday. Which at the moment is Christmas and Halloween. I keep them in labeled, covered totes on top of my shelving.
For the rest of my fat quarters I keep them together in the fabric line (set) they come in. My fat quarters are all fabric lines, not solids, and when I use them, I use the set. If I have orphan ones, I keep them together in no special order, in a tote on my shelf.