I use up my bobbin thread on scrap quilt projects, where the color really doesn't matter. I never use a bobbin as a top thread. When the top thread runs out, you have a real problem. In fact, when I can see the spool quite a bit through the thread that is left, I wind all the left over thread onto a bobbin and use it up there.
Some days I just get the urge or have the time or just feel like it, and I use up all my "almost gone" bobbins. Then I wind a few with thread from "almost gone" spools and keep going. When I'm doing this, I am aware that the bobbin thread is about to end, and keep an eye out for it.