I am looking for energy audit software right now. We have a common problem, a 1973 house with some built-in energy inefficient features of that time. The two biggest problems are single pane glass (with built in storm windows - providing U values somewhere between that of single-pane and double pane) and no insulation in the walls. Both of these are fixable, but at a price.

We are fortunate to have a high-efficiency gas furnace, 5 year old higher efficiency AC system and fully insulated attic (the low hanging fruit of energy efficiency!).

... here are some online energy audit options I have found:

Zip code insulation program http://www.ornl.gov/~roofs/Zip/ZipHome.html
Fast AND easy to use. This program has simple, easy to understand suggestions for us:
1) Blow insulation into any uninsulated exterior wall cavity. R-13
2) Insulative sheathing on empty wall, R-5, but only if the exterior siding is removed for some other purpose - like a very costly siding replacement!
3) Basement wall interior - R-11. An option I am not thrilled with, because we just recently painted the basement. But we do have huge amounts of above and below ground basement wall. Did I mention the house is large?

Rehab Advisor http://www.rehabadvisor.pathnet.org/index.asp
Suggestions:
1) Insulate Attic - Insulate your attic to a minimum of R-49. Install vapor retarders in non-vented framed ceilings. (already done!)
2) Seal Duct Leaks - Have your ducts professionally sealed to reduce leakage to the ENERGY STAR specification of 10% maximum. 1.5 year payback expected
3) Insulate walls
4) Seal Air Leaks - Have a professional seal your home's air leaks. Typically, this reduces air leakage by 25%. Expected cost $554 with a 2.8 year payback
5) Windows and Skylights - When replacing your windows or skylights, choose ENERGY STAR qualified windows with a U-Factor of 0.35 or less and skylights with a 0.60 or less. Expected cost $744 with a payback of 2.4 years. [Clearly, this is extra cost for energy efficiency over the cost of a standard window replacement.]
6) Reflective Roofing Materials - When replacing your roof, choose reflective, light colored shingles to prevent increased heat transfer in the attic.

Home energy saver http://hes.lbl.gov/
This is a very detailed calculator, but it has some slightly confusing results. It predicts that upgrades to our home will drop total energy costs (gas + electric) from $3860 to $1549. The problem is, our actual energy usage is only about $2500 per year. (1100 CCF natural gas and less than 10,000 KWH electricity)

HES suggests Air sealing, high efficiency dishwasher and 3-pane low E argon windows.
Here is what it says about the windows:
"Estimated Annual Bill Savings: $98
Estimated Lifetime Energy Cost Savings: $2940
Upgrade Cost: $1681 above the cost of standard windows
Return on Investment: 4%
Upgrade pays for itself in: 17 years"

The HES program gives conflicting advice on R-11 blown in wall insulation.