I store them in one of the plastic tower storages from walmart. It holds a lot of things since it has 5 drawers so I can store any extra stitch markers I have.
I have a boat load of small project bags that i keep most of my hooks in and the main ones i use are in a case that my daughter bought from me off amazon. it has 2 zippers and a bunch of pockets inside tto store other things like pns and sewing needles.