I have the boxes that are meant to be used for "match box toy cars". My spool of thread with matching bobbin (a small pony tail elastic is around the bobbin)) is placed in each compartment. Spools of thread that have not yet been used, I keep sorted by colors --red/pink/purple, blues/greens/, white/black/grey, yellows/browns--in plastic shoe boxes--marked on end of each box so I can easily get out a new spool of thread.

Here are some more ideas:
I've heard of someone using a Q-tip inserted into the thread spool and the bobbin on top.
You can make custom-made dividers/boxes from plastic canvas. Just cut to size and stitch the sides together with yarn or string.

I too have bobbin box organizers , that I keep by my sewing machine. I will use the bobbin that has little thread left on it for my strip or crazy quilting.

I have some bobbins just in the drawer or boxes with the hair thingies around them but when I want to keep the bobbin with the spool of thread I take a skinny piece of scrap and tie the two together,I still put a hair thingie around the bobbin and put in a drawer.

I use 3" x 5" zip bags that I got at a packaging store in town. But I've also seen similar bags in the candy dept. at grocery stores or craft stores. The ones I have were $1.75 for 100 and I put the spool of thread and the bobbin in one bag. Also I have some large cones that I put a pipe cleaner through hole in the top (and come through the cone) and add the bobbin and twist closed.

Paperprincess, I really like your idea here. Thanks for sharing.

When it comes to storing spools of thread it just drives me buggy when they get tangled. Here is what I do; I wrap a piece of cheap heavier weight plastic around the spool and secure it in place with a piece of tape. Since space is a premium in my house I just keep them all in a large tin. Any heavy plastic will do like window plastic, or some packaging plastic. Might sound a little anal but it works.

for the colors i use a long like pipe cleaner put through both thread and bobbin twist and put into a draw. for white , black, cream left overs i use for piecing i wind as many that will fit into a pill bottle put the lid on and put them in the draw or while i am piecing by my machine . I use only a few pins at a time and don't need the whole box so i also put my pins a a pill bottle that i'm bot
using.also for the bobbin not to unwind I will just cut off
small bit of tape and
tape the end down.

I use a plastic tackle box. They have compartments and I can store the spool of thread along with the matching bobbins.

I was so lucky to find a thread caddy made in Norway that is big enough to hold all my thread and bobbins. It is about three feet high and opens up into several layers. It's just too cute. Found it an antique and collectable store and bought it with my birthday money.