I've just changed the way my glass toys are arranged. Previously, they were stacked laying flat, which made searching for any particular one into a bit of a chore. So I recently arranged them in the trunk so they're all standing on end. Now selection is a breeze, and they take up less room.

You can use one of those shoe dividers, turned on its side, or build the compartments yourself out of wood, cardboard, foam, or whatever's on hand. My dividers aren't quite as tall as the toys, but it still works well. The toys in the cushier bags, like the ones from Don Wands, are positioned strategically between the toys in the thinner SSA Glass bags.