Being an obsessive/computslive wood scrap keepter, I have simply developed a system for storing and stacking small pieces of wood, so that when I need them, I know where they are and can put my hands on them quickly (so that I don't lose my train of thought on what it is I am trying to do in the first place).
When my kids were small, I would take my small scrap pieces of wood and make many geometrical blocks for them to play with. I would make pieces modular (that is, in even multiples of say, 2"), would be sure to round off corners, seal and paint with a non-toxic gloss plyurethane paint and make sure the smallest piece won't fit in the mouth. The blocks included squares, rectangles, trapazoids, parallellograms shapes, pyramids, arches and some flat 1/4" pieces. I then built a carry block box to put everything in. Of all the toys our kids had when they were growing up, they played with these blocks more than any others. Of course, you will have to glue pieces together to get some of the shapes. Also, to keep the mass of the pieces down (less damage caused when they were used as missles), I used only pine.