In a move that’s certainly not going to make fans of the Mac Pro entirely happy, Apple quietly upgraded the pro desktop line today after the Worldwide Developers Conference keynote. And it was a relatively minor update.

The Mac Pro now comes standard with a 12-core configuration instead of eight cores. However, it still has no Thunderbolt ports and continues to sport USB 2.0 only even as the MacBook Pro and MacBook Air move to USB 3.0.

The US$2,499 Mac Pro sports a 3.2GHz quad-core Xeon W3565 processor — which is capable of 3.46GHz using Turbo Boost. The Intel processor supports Hyper-Threading for up to eight virtual cores and has 8MB of L3 cache.

The $3799 model has two 2.4GHz six-core Xeon E5645 processors (Turbo Boosting up to 2.67GHz). It also has Hyper-Threading (24 virtual cores) and 12MB of L3 cache.

The $2,499 Mac Pro has 6GB of 1066MHz DDR3 ECC SDRAM; the $3,499 Mac Pro has 12GB of 1333MHz DDR3 ECC SDRAM. Both come with a 7200 rpm 1TB hard drive. Three other hard drive bays can be customized to your wishes. F

The new Mac Pro comes standard with a 1GB ATI Radeon HD 5770 PCI Express cards. The 5770 has two Mini DisplayPorts and a dual-link DVI port.

Build-to-order options for the $2499 Mac Pro includes a 3.33GHz six-core Xeon processor (this will cost you an extra $500). You can add a pair of 2.66GHz, six-core Xeon processors for $1,200 or two 3.06GHz six-core Xeon processors for $2400 to the $3499 Mac Pro.

The Mac Pro Server has also been revved. It costs $2,999 and boasts the 3.2GHz quad-core Xeon W3565 processor found in the $2,499 Mac Pro, but the Server includes two 1TB hard drives, 8GB of RAM, and OS X Lion Server.