The reccomendation from the power company in my area is to install the 80% furnace and the highest SEER rating HP that you can.
From what I have seen the cost difference in 80% and 90% is about $800. If you are just looking at cost - you won't get the additional money for the 90% back in savings (You are talking 10% savings on the couple of days a year that the furnace runs.). Now, in my house they may need to redo the brick fireplace to get the venting right. If they do that the 90% would be a better deal because it vents with PVC pipe.
In general this site might help you http://www.energyright.com/index.htm.