i used to keep mine in color family but also by size. pieces that were large enough for backings were kept in color families, too, but separate from the ones that were only 1-3 yards.
I recently reorganized and decided I needed a new way to organize so I was likely to use my stash (I do not have a huge stash, by the way, so this likely won't work for those who do...). I grouped my fabrics by ones that I planned to put together in a quilt. that way, when I felt like making something new, I can just pull out a set of 2-5 fabircs that are already ready to go. Then the leftover fabric that I didn't find a "home" for using this method, got color coordinated in a more hidden spot.
I keep my solids separate from my prints.