Ignore flowrider. He not very knowledgeable. Even if you but a 2009 single core and eventually want to upgrade to dual cores, then you are stuck with a 2009 CPU tray as the 2010, 2012 trays are incompatible. Stay away from the 2009 and flowriders advice.
flowrider's advice is 100% true. In fact, he's one person I would trust above most people for help with Mac Pros. I have a single CPU 2009 Mac Pro, its bone dead simple (for me anyway because I'm a hardware guy) to replace the processor in it. Its a standard LGA socket and bracket where you can uses lidded CPUs, whereas the dually 4,1s have the odd need for de-lidded CPUs.
True, you cannot swap the proc board in a 2009 for a 2010 or 2012, but last I checked the 2009s were cheaper and single CPU models are easy to upgrade. I have changed the processor in mine three times with no issues.
My recommendation is get the Quad Core 2009 (4,1) machine. Upgrade the firmware to the 5,1 then swap in a Hex-Core CPU. I have a 3.33GHz Hex in mine and it just slightly out edges my Quad nMP on Geekbench Multi-Core (but I found FCPX rendering and exporting to be faster on the nMP). The 4,1s have been seen recently on eBay for as low as $450. I picked mine up from a recycler for $40 but it needed a lot of work.