I think everyone agrees that the A64 is a great CPU and that AMD has the upper hand in processor technology at the moment. If a buyer is not very price-conscious and always wants the latest and the best, then an S939 A64 would be the way to go.
But most of us have to balance price against performance, and 64-bit systems cost significantly more than, say, Athlon XP systems. Especially for those who have to make do with on-board graphics at least for the time being, there are still no 64-bit motherboards with on-board graphics that can even come close to an nForce2 IGP. For reasonable gaming experience, a separate graphics card is a must for a 64-bit machine.
Therefore, the difference in total cost between a 32-bit system and a 64-bit system can be much more than the cost difference between the CPU-motherboard combinations alone.
If one is thinking of future-proofing against the advent of 64-bit softwares, those are still a few years down the road, and by that time a current bleeding-edge machine will have become decidedly non-cutting-edge.
Conclusion : if cost is not a big factor for you, buy a 64-bit machine. If it is, go for a 32-bit system and spend the money saved on a good graphics card or something else you need.