Cardboard with labels and diagrams and bolts stuck through is good.

In aviation I use small fabric bags and a paper label to mark them, tie them to the part I took them off

At home I use a bunch of small plastic containersfrom the same maker. Bolts from each component get tossed in their own box, slap on some painters tape to mark them and stack the boxes. That way they take up minimal space and are still organized.