That's a tough one. You can get substantial energy reductions by following energy-efficient building practices for both the roof area and the windows of a building. Research has shown that heat from the windows actually puts a bigger load on the air conditioner than does heat from the roof area, but my own preference is doing things to the roof. I like the opportunities there.
Radiant barriers work great.
Good attic ventilation keeps the house more comfortable and lets you use the attic for storage. A clean, light-colored roof looks nice. And stopping that heat from the roof and attic from getting into the building will keep everyone more comfortable and use a lot less energy in the process. Speaking of the role of the roof in energy efficiency, I read an article recently about the design of the new Denver International Airport, which features a special fabric roof in an energy-efficient design. The airport has gotten a lot of bad press in recent months because of its faulty baggage handling system, but the rest of the place seems to be well on track to being comfortable and efficient.