I doubt that what I have done would suit anyone else, but I will tell you anyway. All my thread is stored in containers where they can't get dusty, etc.; I have different places for different types of thread. 100% cotton sewing machine thread is in one plastic 3-drawer unit; dual duty in another; polyester embroidery thread in the drop-down-door section of my book case; rayon cones in a plastic box under my bed; rayon spools in plastic storage boxes (stacked), each box designed for a specific style spool. It doesn't sound very organized but, in fact, it is because I know precisely what thread selection to look through. Because I have hundreds of machine embroidery thread colors, I keep a typed up-to-date list of the color numbers and where each one can be found.