If you get an auto, go with a 6. 7. The 68RFE is a much better trans than the 48re, atleast stockwise. If you plan to add a bunch of power (more than a downloader or box) then skip the auto or stick to an 03-07 5. 9. The 68RFE is still questionable with added power. 6. 7 needs to have DPF deleted and EGR blocked off, and an H&S or Smarty for code-free deletes.
Best mileage would be 03 or 04.
Most bang-for-your-buck would be 04. 5-07; they will always make more power than a comparable 03/04 or 6. 7 with relatively minor mods (programmer, intake, exhaust, etc. )
Love my 03, and love my 07. Cant go wrong with any 3rd gen in my opinion