This is how I store most of my embroidery thread. It is in the corner of my sewing area -- away from light and heat. I have it sorted by colors where possible. The bottom area has my embroidery thread bobbins and bobbin spools as well as my hat and other attachments.

The shelves were on sale at Target when I got them. They lock into each other with dowel bits. I am sure you could use many things to get the same results. I wanted my threads up where I didn't have to bend over to get to them or see what colors I have. The shelves sit on top of a file credenza. The cases for the threads were from Jo Ann's (also on sale). It has been wonderful to have them like this.