For all my smaller jigs I made a couple boxes like the Clam Ice Armor boxes. Just small boxes I had around, cut all the dividers out and glued foam in.
For anything larger or with multiple hooks that are tough to secure I hang them in a spinner bait box. The one I carry is about 8"Lx4"Wx4-1/2 - 5" deep. I has 4 dividers in it, with 10 or 12 notches per divider. As TType mentioned, I can't fit everything into the one box, but it lets me take 20-40 (depending on size..) spoons/jigs/whatever without them getting chipped and tangled!