That probably depends on how many windows you have to replace and how experienced you are. I am in the process of replacing 9 windows in an REO. I decided I need to do this before I move in since a few of the windows are broken. It is helpful that this will be a single day job for a crew with the window company. But I am paying over 100 extra per window for the installation.
I would not be surprised if the government tax incentive for energy efficient windows has allowed window companies to increase prices, but I was not pricing windows prior to the tax credit. For companies that don’t separate installation and window cost in the billing, I am told the IRS allows the 30% credit to be applied to 80% of the bill (24% of the total). If true, this implies the IRS believes 20% installation cost is normal (or an 25% of the window cost).
Of course the other option would be to buy the windows, then hire guys with experience to do this on the side for less. For me there is something to be said for the company measuring and installing the windows. That way, any problems or errors would have some recourse.