The arguments for S939 so far are as follows:
1) Better overclockability/more frequency headroom
2) Better upgradeability/more "futureproof"/cheaper in the long-run
3) Better heat/power output
The counterarguments for S754 so far are as follows
1) 90nm Semprons can overclock about as much as their S939 Venice/Winchester counterparts
2a) It's cheaper to get an S754 now and use the money saved to get better associated hardware.
2b) The user is able to sell the S754 mobo/CPU and pay a marginal amount to upgrade to a S939 platform in the future
2c) S939's upgradeability is moot since most of the time you'll need to upgrade the rest of the system anyway.
3) Semprons have lower heat/power output
However, I think that we should segregate the CPUs into different classes, as mentioned by others in previous posts.
In the low end side, there's no doubt that S754 is the obvious choice since Semprons are cheaper, have lower power/heat output and some are highly overclockable as well. The price/performance ratio favors S754 systems, and at the low end, price/performance ratio rules.
In the high end side, S939 systems are also obvious since the FX series CPUs are currently the fastest systems. Overclocked, they are even faster. The fastest S754 CPU right now is a 3700+, and since these are 130nm cores AFAIK, they won't be as overclockable.
The controversial range is the mid-range section, where there's an overlap of S754 and S939 CPUs. In this range, argument 1 and 3 doesn't really hold for S754 sytems since the overlaps occur only in the A64 CPUs, and AFAIK the only S754 A64 CPUs are 130nm ones, hence they won't overclock as well, or have as lower a power/heat output as S939 CPUs. Therefore, S939 wins in overclockability and power/heat output.
However, argument 2 is still debatable. It's not entirely clear which platform will be "cheaper" in the long run. If you're one to upgrade frequently, S939 might have a few breaths more because there are a few more iterations of CPUs coming out for S939. However, if you upgrade say once a year or longer, then it depends on other factors such as the need to upgrade memory/graphics card. S939 still offers a choice between sticking with your existing platform and just plugging in a new CPU. Obviously this won't be ideal since a year from now newer and faster chipsets/memory/video cards/HDDs will be available. A S939 system now might not have SATA3/PCI-e 32x/DDR-3 support/etc. However, the choice is still there to upgrade just the CPU. As for the S754 system, the choice isn't there since AMD has made it clear that 3700+ is the end of the line, so unless you start out with a <3700+ CPU, that's as fast as you can go. Of course, you can sell your existing S754 system pay a marginal fee to upgrade to a S939 system, if you don't mind the hassle of finding a buyer and finding a "old" S939 in the future. You could also leapfrog the S939 system for whatever new system there is, and pay a price premium. However, if a user is starting off with a S754 system in the first place, I doubt he'd be willing to pay a price premium. Finally, if you're going to keep your system for a while(2+ years) without upgrading anything at all, then S754 is the obvious choice in the mid-range since it's cheaper and performs almost as well as its S939 counterparts.