We have found that high efficiency furnaces (up to 95%) have a cost/benefit ratio that decreases exponentially as the efficiency increases above this level. 
Simply put, the reduction in operating costs offered by higher efficiency furnaces is normally not justified by the increase in the initial purchase price. 
These furnaces typically will include other features that may enhance comfort but from a strictly return-on-investment point of view the extra cost is almost impossible to justify. 
If you are in a colder climate we do highly recommend the 95% efficient furnaces for the lowest possible energy costs.