Recently, we built a Supermicro Workstation 7047GR-TRF configuration. I am revising the system configuration to update the parts to get a comparable overview:
Supermicro Workstation 5037A-i - $580
Xeon E5-2643 v2 (fastest available) - $1552
Memory (4GB/ECC/DDR3-1866 x 4) - $240
Firepro W8000 (x2) - $2560
Intel SSD 910 400GB - $2000
Windows 8.1 Pro - $140
Others Accessories - $100
Total - $7,172
The base system will be pretty much high vs the $3,999 cost
In another comparison
Supermicro Workstation 5037A-i - $580
Xeon E5-2697 v2 - $2750
Memory (16GB/ECC/DDR3-1866 x 4) - $840
Firepro W9000 (x2) - $6800
Intel SSD 910 800GB - $4000
Windows 8.1 Pro - $140
Others Accessories - $100
Total - $15210
The configured system is still pretty high compared to $9599 from Apple pricing
Although specifications cannot be matched one is to one, I believe that the Windows workstation can be reduced in pricing by changing the Intel PCIe SSD and GPU to avoid using the top of the line products.
For example, using the following
Supermicro Workstation 5037A-i - $580
Xeon E5-2697 v2 - $2750
Memory (16GB/ECC/DDR3-1866 x 4) - $840
Quadro K5000 (x2) - $3200
Intel SSD DC S3700 200GB - $500
Windows 8.1 Pro - $140
Others Accessories - $100
Total - $8110
The configured Mac Pro is $8119 for the 256GB Storage and Dual D500.
So I guess the configuration will depend on the system.
For us though, we have found a more cost efficient alternative by buying a Supermicro 7047GR-TRF dual Intel Xeon socket and not using the top of the line for everything. But we are able to achieve 12 cores 2GHz, 64GB RAM, Nvidia K4000 for Display, Dual GTX680 GPU for compute, 8Gb FC Celerity HBA for around $5,000.00.
It will really depend on the applications to be used at the end. For us though, most of the applications are available in Windows and Linux configurations will limited Mac exclusivity so the PC solution is economical for us.