The main reason I see for holding off is if you're looking for a better future upgrade path than if you went for a system right now (true for both AMD and Intel, I presume, with Conroe coming). I do think that the initial benefits of the AM2 platform will negligible and possibly not noticeable, as it will take a while for things to 'settle down'.
If you get a bleeding edge system now it will last you for a while, and by the time you're ready to do another upgrade things will have sorted themselves out on the new platforms.
While the downside of a S939 system is the limited future upgrades of the CPU and possibly RAM, the upside is that it is a very mature platform. It will take a while for AM2 to reach the same level maturity.
Generally my approach to the question of "now, or wait" is "now". There is always something on the horizon that makes you think it's worth waiting. Get what's availalbe now, and enjoy it until next time around. That's what I just did, anyway, so at least I followed my own advise