Now I'm sure someone who knows AMD can put something similiar together for you to consider.
My two cents.
The thing with the AMD system is, as mentioned, the cost of the motherboard is generally lower. The AM3 socket series uses dual channel DDR3 modules in a 2/4/8 configuration.
AMD has a slight advantage in the system complexity department, that being the memory controller is on the die of the Phenom, not on the motherboard, and it cuts down on the board's "real estate requirements". Less circuit traces and layers mean reduced cost of the board.
Another tangible benefit of AMD is when using an AMD chipset motherboard, rather than an Nvidia chipset, there seems to be a smoother interface to the graphics hardware, and some motherboards can even Crossfire the onboard GPU with a discrete card. It's called Hybrid Crossfire, and depending on the motherboard and card combination, you can get decent performance out of a cheap ATI Radeon card. No surprise, since AMD owns ATI, that they would optimize their platforms for their own equipment. :) Nvidia boards also have a Hybrid SLI on some models, as well, but I have never seen a side by side comparison.
A big disadvantage to AMD systems is the lack of memory divider options on most motherboards. Intel rigs allow much more flexibility in how the memory and FSB speeds are strapped and divided. This can lead to some serious gains in performance, particularly when overclocking.
Overall, my take on the new six core Phenom is that it's just "meh." Most apps can't even take advantage of a quad yet, and few users use the kind of software that would really benefit from one at this point. Right now, it's just "Core Wars" from both, and it's a pissing contest to see who can get the most cores on a die.
For my money, rather than the Thuban core Phenom, I would rather just put my money into a good quad like the Phenom 955 or 965, a good quality motherboard, and some fast RAM. You can always upgrade to the six (or eight, or whatever comes out next, as long as it's an AM3 socket) core model later, when the core contest is over and the market stabilizes a little.