If you were speccing a deskside compute box (something like a quadcore XEON or Opteron and a bunch of RAM) to run code that is not highly memory bandwidth dependent, would you worry very much about it using DDR2 vs DDR3 RAM?
Going with newer machines that use DDR3 is more expensive and I don't see that there is enormous difference in performance between DDR2 and DDR3 outside of perhaps raw bandwidth.