converting single pane windows to double pane
I've done this myself and I can relay my experiences. Doing this over the average of the two years I looked at about 10% difference in my heating bill. I replaced the windows with 1/4 glass with a 1/2 inch gap. My method was to use the original wood molding to rest the first replacement window on. I used glazing fasteners and then filled all gaps with silicon caulk. This was after insuring that the wooden window frame was is good shape and free from rot, defects, and loose joints. ANY air that pass through will be a problem for more reasons than just your bills.

After setting the first pane I surrounded that pane with 1/2 by 1/2 inch oak stained the same as the interior of the windows.I set this trim in a bed of wet silicone at the corner of the first pane of glass and brad nailed it into the window frame. I then set the second pane of glass using fasteners and silicone. It has worked really well except for one window where the joint failed and allowed moisture into the air space between the two. One moisture is in there you'll have to undo all the work and start over. Like wise only the interior window will be easily replaceable, if something breaks the exterior pane you'll likewise have to tear it all apart. For me its worth it. 

I have a 118 year old home and I like my old double pane windows. Aluminum windows on this house would be a crime.