i store my thread on thread racks (purchased at JoAnn's with a 50% coupon) attatched to the wall.
I put clear plastic over them to keep them clean. Since the pegs are short, I cut straws, fit them over so I can put my bobbins on the top of the thread. It really works well and I can see immediately what I have. Extras are in drawer. I keep all of the embroidery thread on a rack , cottons on a rack and the regular sewing thread on a rack.