Storm windows
 

Can you use storm windows with double pane windows, or will the heat trapped between the two cause the seal on the double pane windows to fail?

Why would you want to do that? All you should need is the double paned window.
I can see condinsation being more of a problum then the heat.

Because a pane of glass for a storm window is cheaper and easier to replace than a double pane window. We can get some pretty sizeable hail and occasional windblown debris that has cracked our storm windows before.

There's two differant companys that make what's called hurricane windows.
There a super tough vinyl film window that when installed look just like reguler double or triple hung windows.
One name is Custom and I forget the other name. I tryed to look them up for you but could not find any info.
There great if you live near a golf cource, the balls just bounce off with no damage.

http://www.bondedvinylwindows.com/id82.html

I would think you would increase R value