unorthodox approach to window upgrade?

LowE is not a single pane of glass
LowE is a glass assembly with argon gas in between
Adding extra panes will help
But you can get fog/condensation in between the panes of glass
I'd install real windows or storms on the outside

Actually it's the glass itself which is low E (different types of coatings are applied to the glass pane.) http://www.energysavers.gov/your_home/windows_doors_skylights/index.cfm/mytopic=13430

http://www.askthebuilder.com/B97_Low_E_Glass_-_Types_and_Benefits.shtml

Argon (or krypton - even better) fillers help reduce heat flow and insulate and increases energy efficiency, though from what I've read not as much as the glass itself.

Trapping moisture in my scenario would be an issue like you mentioned. Not sure if there's a practical way to avoid that, so the cheap glass sandwich idea may not be a good one for that reason

You would need to purchase a sealed unit of glass to be effective.
Ron

As the previous poster mentioned, you need to get sealed panes or you will have problems with moisture buildup and fogging. You should be able to get units made exactly to the size of your opening in double or triple pane, low-e, argon, etc. Your local lumberyard or window supply company should be able to measure and give you a quote. You will just have to remove the stops and install the new panes.

If the heat buildup is due to direct sun on unshaded windows then I think a piece of lowE glass would work. Simply leave a small air space for any moisture to migrate out. If you need actual thermal efficiency then new windows might be better. Another option if direct sun is a problem is to install a shade cloth on the outside. You can make a roll up assembly to get them out of the way when wanted. I did this on a house I once owned that had single pane windows facing west. It worked very well and made a huge difference on the heat load of the house in the evening. You can get different levels of blockage up to 80% I believe yet still see through the material.