Is there a good way to store and organize try/combination squares?
If all your tools are steel or other ferromagnetic material, I would try something like this: 



It's a magnetic knife holder that you should be able to buy at any kitchen store.

Alternatively, you could build something along the lines of a traditional knife block by glue-laminating pieces of wood and leaving appropriate gaps for each square.  Although, some types of squares might not fit.