I had some 1/2" plastic water pipe (PEX pipe), and decided to cut it up and fill one of the compartments. The inner diameter of the pipe (7/16") is a perfect size to accommodate all of my bobbin tubes/handles. It is also large enough for most tools (scissors, bodkins, tweezers, etc.). The pipe is also very cheap. Five feet of this stuff was only $2.79 from my local Ace Hardware store.
Here is the compartment, after filling with section of plastic pipe. I used a couple pieces of packing foam along the right edge, to hold the pieces snugly in place.
The plastic pipe is easily to cut. This tool cuts square the plastic, leaving a nice smooth edge (no burrs to catch on things).
Here is the organizer, loaded up with bobbins, various waxes/glues, and dubbing boxes.
Overall I am happy with the finished organizer.