Jack - you work with large files all the time, what are your thoughts?
With the current generation of Mac Pro's, it's really a tough call, but here are my thoughts:
It seems that Photoshop CS5 cannot efficiently utilize more than 4 cores, so core speed becomes more of a consideration than total number of cores. Core speed is a linear performance gain, and since you can get a 12% faster processor (3.33 vs 2.93) in the single 6-core configuration, this would seem best suited to Photoshop. But now you're limited to 4x8G or 32G RAM. At first this seems like a limitation over the 12-core machines 64G potential, but the reality is that many benchmark tests actually show an efficiency falloff for RAM, so 3x8G for 24G in the 3.33 6-core machine regularly BEATS 32, 48 and even 64G in the 2.93 12-core box. Hence, logic dictates that the 6-core 3.33 with 3x8G RAM is probably the current sweet-spot. At least for Photoshop...
However, if you step up to software that utilizes more cores, all bets are off. Fortunately (or unfortunately depending on your point of view) there are not very many pieces of software that utilize more than 4 cores effectively other than for high-end video processing. And C1...
So if you're a Phase shooter, which the OP is, it creates a sort of dilemma. What I do know, is that the net real difference between running C1 on the 4-core 3.33 and a 8-core 2.93, was about 20% faster on the 8-core machine. Assuming that trend holds for the 6 and 12 core machines -- and I'd guess it's a little less of a difference, so call it 15% -- then were talking saving maybe 1 minute for every 6 or 7 minutes of actual batch processing. So I'd need to factor in how I use C1 and Photoshop --- and in MY case, mostly I toggle C1 to process an image in the background while I'm searching/editing other files. And of course I then when I do batch in C1, I'd have to wait a bit longer on a machine with fewer cores.
Next I factor in how much time I spend in C1 versus PS. In my case, they're about equal, and given the PS gains on the 6-core box about equal the C1 gains on the 12-core box, it is kind of a performance toss-up for me --- though it may balance differently for you. For the rest of the stuff I do, either configuration is plenty fast enough for the amount if time I use it, or way overkill for things I do all the time, so not even worth a worry.
But there is then the cost consideration, and it's not trivial. The 3.33 6-core box is about $2400 base cheaper than the 2.93 12-core box -- and that $2400 will basically pay for 24G RAM (3x8G RAM is $900 at OWC), AND 3 200G RAID edition SSD's ($600 each at OWC), making it a very attractive choice indeed!
So, my humble two-cent conclusion is: It's a close-enough call between the 3.33 6-core and the 2.93 12 core on performance, that given the cost savings I'd opt for the 3.33 6-core machine if I were buying today.
Hope that helps,