Seriously - if they're puttied and caulked, they're not really that bad. But insulated shutters keep light in at night, too, and the benefit is that they don't affect the outside appearance of the windows, which is really an important issue if you have traditional windows. For me, anyway.
There's a whole long list of energy conservation measures here, including many ways to improve the insulation values of windows. Most of them are lower in priority for me than sealing up the myriad holes in the basement (including several windows that are inexpertly boarded up), but the shutter thing is really intriguing. I have two big pieces of Styrofoam left over from the carriage house family room floor that are serving as insulation right now in my office, but it's not a particularly permanent solution.