The main differences between the 2006 and 2008 mac pros would be:
- improvements on the FSB (speed bump + better handling). But for a single quad, that may not matter much, because that was more a bottleneck for the dual quad than for the dual dual.
- futureproofness (more PCIe lanes on the 2008, 64b vs 32b EFI, but relative, as both mac pros are incompatible with nehalem). I'm not sure apple will provide custom rom for future video cards for the 2006 mac pro (since the mess it was for the 8800gt), but I'm guessing the future pcie cards for the next mac pro will be compatible with the 2008 one (pcie 2.0, 16x and 64b EFI). But with Apple's history with video cards, who knows?
- power consumption. I'm guessing the 2006 will consume more power with 2 cpus than the 2008 with one, but that would have to be confirmed.
Anyway, that depends on the price you can get each one.