I would say long term the new windows are the best route. I believe the energy savings year after year is going to exceed the energy used to manufacture and deliver the new windows. (assuming you buy energy effecient windows of course)
I replaced my doors and windows a couple years ago. We have 3 - 8 fooot sliding glass doors in the back of our house. They were expensive to replace but our home is much more comfortable now and there's been a dramactic reduction in heating and cooling costs.
Greener People for a Greener World TM