I currently use the pony tail holders but I'm going to switch to the clear poly tubing. We use the tubing in our business and we always have off-cuts that would otherwise just be tossed. I asked my husband a while back to bring some home ... I guess we both forgot about that request.
I keep my thread in a clear poly sectioned tackle box (made in the US too!). I have several boxes that stack and I have labels on the outside of the boxes stating the contents (two boxes of 50wt Aurifil). If/when I have a bobbin with thread still on it I pop into the same section as the thread.