I recently specced a system quite similar to the Mac Pro. I used a SuperMicro motherboard, a similar Xeon 6-core CPU, 128 GB of ECC RAM, two Samsung 512 GB Pro SSDs (primary and a local backup), and an NVIDIA Quadro GPU. All the other components (case, power supply, CPU cooler, fans) are top quality. My supplier ordered the parts and charged $100 to assemble and test it. The user is running Linux and he's happy with the system - happy enough that he's demoed it around his department and says it has generated much interest. In any case, a new Mac Pro wasn't an option for him as he's using CUDA rather than OpenCL.
The total cost was $4,150. The system has twice as much RAM as the Mac Pro supports, an upgradeable GPU, space for many more drives in the box, and a savings of about $1,500 over an equivalent Mac Pro with 64GB RAM. OK, the box doesn't look as nice, but since it's under the user's desk that's not so terrible.
The cost saving is not the biggest improvement over the Mac Pro. The big items are having an upgradeable GPU and expandability inside the box - Thunderbolt just doesn't have the product base yet. I'm beginning to doubt it ever will with higher speed USB in the pipeline.