Little late, but...
It's going to depend on what you want. S754 is still a perfectly viable platform. The performance difference between 754 and 939 is not MASSIVE (although it's not completely insignificant either)... the deciding factor should be upgradeability. If you want a system that you can upgrade 6 months or a year or two down the road, you NEED to be going with S939 AND with the nForce 4 chipset (which will require a PCI Express graphics card).
PERSONALLY, I went with S754. I didn't even intend to buy a single cpu A64 system (I was planning on buying a dual opteron this summer) but I found an ES A64 on ebay, which was s754, and which I had to have. So I bought it. And a board for it. And promptly killed the CPU by dumping ~4.5v into the memory controller... luckily, the guy that sold me the ES happened to have one more... which I also bought. And haven't gotten around to testing yet (too lazy to pull the sempron to put the es in). Upgradeability was a non-issue for me as the whole reason I bought the system was to run the ES. And I had no concerns about how long the system "lasted" before it became outdated. I buy a new computer every 6 months or a year anyhow, and they're usually upgraded several times between each new build, so... The A64 ES was just a toy. Just something else to add to my collection of weird, unique, and/or hard to find computer hardware.