I did the "photo storage box with upside down golf tee's in the bottom" method and it works great (no dust/no light) and they stack neatly. However I do like the idea of the peg with re-arrange-able dowels.
I store my normal sewing threads in a tackle box that allows me to rearrange the sections. This lets me make the section big enough for the spool and my matching bobbin. But with the dowel method ShirlinAZ mentioned I could combine the two since the dowels would be long enough for bobbins on the top.