In 2009, Apple produced the Mac Pros with only Quad-Core processors (single processor quad-core and dual processor 8-core).
In 2010, Apple started producing the 6-core and 12-core Mac Pros using the 6-Core processors (single processor 6-core and dual processor 12-core). Thus, in 2010, Apple updated the architecture of the dual processor board to work with the dual 6-core processors since they are physically different.
For the 6-core, going with the 2009 is perfectly fine because the architecture of the 2009-2012 6-cores are 100% identical. The only physical differences between the 2009 and 2010 6-core are:
• 2010 comes standard with an Airport Extreme Wireless card while it’s an additional option on the 2009.
• 2010 comes with an ATI 5770 1GB graphics card while the 2009 comes with an NVIDIA 512MB.
For the 12-core, we recommend going with the 2010 genuine 5,1 since there is an architectural difference between the 2009 and 2010+. The 2009 12-cores function perfectly fine; however, the 2010+ 12-cores are more architecturally solid.