I use the thread boxes from Connecting Threads for spooled thread, a flat plastic container to stack cones on layer deep, rubber ring for neutral thread on bobbins for each machine, and small plastic fishing tackle case for colored thread on bobbins. Connecting Threads box and fishing tackle case open on both sides for easy access.
A separate flat plastic box holds specialty threads either in medicine bottles or plastic bags. Nylon thread with bobbin in medicine bottle; hand quilting thread in plastic bag; buttonhole and carpet thread in another plastic bag.
My rules are: visibility, accessibility, and no tangles!