I either use them up piecing something or binding something....

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.

I use them for handpiecing and applique. My bobbin thread is always Bottom Line which my Jems will not take as a top thread, otherwise I might use it up as a top thread.
Rarely do my top thread and bobbin match; I tend to use gray, cream or ivory for all my machine work. If it's a very dark fabric quilt I'll use a dark Aurifil on top and a dark Bottom Line in the bobbin, doesn't matter what the actual colour is as long as it's dark.

:D Then you just have more bobbins with little bits of thread. --- Ask me how I know. :D :D Seriously, I just use them up when I'm piecing.

I save all my bobbin and cutoff threads in a box. I found a pattern to make ornaments by sandwiching the threads between water saluable stabilizer (spelling?), stitching all over, disolving the stabilizer then cutting out shapes, starching and ironing flat. Then hang. With alot of colors the ornaments look somewhat like lace. I don't have enough thread yet but getting there. They need alot of color, metalics, maybe some yarns for texture.

I admit it, I throw 1/4 full bobbins and under in the trash.

I use the thread off of them when hand sewing the bindings on my quilts.

I use the left over threads to make fancy cords to use for embellishment.

I have lots of bobbins, so I save them and use them up as I go.

I. Found this idea very interesting, thanks