It sounds like you'd want to be able to use your phone like a cd drive and run the program off of it... correct? Not on the phone itself, just from the phone on a PC? Which program?
Well, depending on the size of the actual exe and also the amount of data it requires, you may just be able to copy the install folder off your pc and onto your droid. Or, if you felt so inclined, you could image the cd and run the image from your phone. Is it just an executable or is their a lot of external data?