Here in North Carolina there is not much of an upgrade. Most of the things that used to make Energy Star expensive are now required by code -- low-E windows, 13 SEER HVAC, etc.
The only additional measures are the air sealing, blocking and backing up of knee walls required for the Energy Star thermal bypass checklist. Although this work needs to be done properly, it is not very difficult nor very expensive -- mostly a lot of caulking and foaming joints in the exterior walls that can be performed by just about anyone. Most insulating companies are now performing this for a pretty good price since they are already on site anyway.
The only other additional cost is the third-party inspection and certification. Everyone charges differently but typically in the $500 range. We are building 3,500 sf to 5,500 sf and spending less than $2,000 extra to get them Energy Star certified. The cost will of course depend on your design, amount of knee walls, etc.
If you are considering Energy Star, you will probably want to look into upgrading your insulation as well. The codes are getting ready to change and increase all of these anyway, so it would be best to go ahead and upgrade to keep up with the future construction. Once you build a tight home, you should also look into adding some fresh air ventilation. There are many different types -- from low-cost using an existing bath fan up to installing an ERV.
This is true for the rest of the year and next year.
In 2012 both Energy Star and the building codes are going to change and at that time there may be a bigger upgrade to do Energy Star. As of now, it is a no-brainer, money well spent, will pay for itself in a few years.
For more information:
Check out architect Polly Osborne's answer to the question "How much does green construction add to the cost of a new home?"