Conroe represents a change in design concept that should improve CPU performance, and reduce heat dissipation.
AM2, at the very least lays in the ground works for AMD's next generation CPU, the K8L, in 2006. Not much difference in performance between AM2 and S939, as AMD has admitted before. But faster Athlon 64 X2 CPUs will only be released for AM2. I don't believe there will be anymore CPU models for S939 otherwise they would be competing against AM2.
I am personally delaying my upgrade until I see plenty of retail Conroe reviews.