Mine are roughly organized in sets of what would look good together in a quilt. If I organized mine any other way, I would be quite lost when it came time to pull fabrics together for a quilt. I also have a stack of "loner" fabrics which do not go with anything else that I own (yet). Hidden on the back of a deep shelf is a hodge-podge, mostly stuff that was given to me: fabrics that I dislike for a variety of reasons; fabrics that I cannot visualize in a quilt; a few theme fabrics. From this group is where I pull practice fabric, etc.
I don't have a big enough stash for it to get out of control. I pretty much know what I have and where it is.