The plastic containers used for push-up deodorants can be recycled into excellent holders for items like nailsets, small drill bits or saw blades. The containers have easy-to-remove caps, and you can push up the bottoms to expose smaller items. Use a felt-tipped pen to mark what's stored inside.
Just about all toolboxes have tote trays. Tote trays keep smaller tools and parts separate from larger ones. If a large percentage of your tool set is made up of smaller tools and pieces, perhaps it’s time to look into getting a multi-drawer tool chest. Slightly larger than a toolbox, it allows you to divide and organize small tools into groups that can be quickly located, collected, and returned.