I use the rubber round bobbin holders for the neutral thread that I use for most piecing. I have bobbin boxes for the more common thread (sorted by fiber content) that I use for fmq, but some specialty threads have the spool and bobbin in a floss zipper bag and are on a ring.
Most of my thread is in a collection of stacking boxes that ;ock together (from Joanns). I use larger boxes for the big spools.