Michael Foster http://www.progresscommercialglass.ca/
As with many home improvement projects, it's always good to get multiple estimates to compare. You may be limited as to your replacement windows based on what the City of SF will allow you to replace them with. Are you still wanting to keep with wood sash windows? You can replace them and keep the same style while having made with double panes. They can be expensive, but they may achieve your goal while maintaining the exterior integrity of your home. Otherwise, you'd be looking at vinyl windows such as the Marvins.
I had a client replace his single pane wood windows and if memory serves me well, he paid somewhere in the area of about $600-$800 for both sashes (one window, top and bottom), installed. They also came out afterwards to do adjustments once the windows had time to settle and adjust to weather.
Zephyr Real Estate
If you buy cheap windows, you will notice the tracks filling up with dirt, and very hard to clean. You will hear them move as they breathe in strong winds. The worst new double panes are dramatically quiet compared with old single panes, and they are functional, but they won't improve your property value.
For windows which do not require additional storm protection (shutters) the price quoted for 50 Sq feet is not unreasonable. However, since the windows are NOT 50 SF but are comprised of six individual windows, this cost seem high. Is other structural work being done? Does this include qualified storm accessories such as shutters and the securing hardware?