AM2 is so much better simply because of ddr2. that's the only big change. the architecture on s939 and AM2 aren't very different i don't think. ddr2>ddr. that's basically the major difference lol.
If you're building the comp down the road go with the AM2 architecture, but if you're building it now go with 939 socket. It's still pretty good bang for your buck.
AM2 is really the way to go. Motherboards are a bit more sparse and more expensive, but that will all change very quickly as it becomes mainstream. I have a question myself: are prebuilt computers beginning to come out with an AM2 socket option yet?