The common buyer gets a new system, not parts. They do not overclock.
A s754 3200 will outperform a s939 3200.
Perhaps for you, spending more, for options like chip upgradeability, and enhanced OCing is worthwhile. For the person who only builds every 2 to 3 years, buying a s939 setup, even at the same price would be spending $ for less.
I just put together another A64 system. I again went s754. I will probably replace that system next year. Just the same, there was no quality option in 939 that would have fit the user's (my daughter) need as well, in the same price range. Next year, she will switch to a PCI-exp graphics solution. At that point, s939 may be a better option. Of course, around the same time Amd says they will change to DDR2. She may go that route, if it fits the cost/use scenario.