MY05, just about the best trade off for good parts, power, reliability, etc. From the engine persepctive had the better valves and valve seats, the electronics had most of the issues worked out, had the most power and TQ in the 5. 9 series.
Early 05 had the NV5600 with no DMF, probably the best manual option available. However, plastic end tanks on the CAC's need a hard look and possible replacement. The late 05's fixed the CAC back to metal but then the DMF and G56 were the only manuals available. The NV had a btter OD ratio at . 73 than the G56 at . 79. With the standard 3. 73 gears the G56 was a heavy toter and not a real good DD unless you want to go with 35" tires or regear.
The drive train from tcase back was about the same on all the models 04-07. MY03 had some issues with diffs and QC that was fixed by 04. The early engines were not as powerful and problems with valves and seats. That again was fixed by the time the 600 series engine came out.
The 04. 5+ turbos are much better, comparatively, thean the previous years. Full 4" exhaust with a CAT that does not generate much back pressure.
The 05+ autos all replaced the TV cable with a motor. Trade off is they were more sensitive to light footed driving styles. All the 48RE's are a good heavy trans with the 05+ models fully capable of using an EB. OD ratio of . 69 makes it excellent for DD and towing to the GCVW. Coupled with a slightly larger tire they are pretty efficient.
The 06 models introduced the TIPM which can be a problem for people who pull trailers a lot. Very easy to burn out a circuit and require a $700+ fix to get blinkers and other circuits back on line. The 05 and older models still had a seperate FCM and PDC that could be serviced independently. They also seemed a lot more tolerant of loads from trailers and their wiring problems.
The 06. 5+ switch to CAN bus for communications. Enter increased cluster controller failures, ECU problems, and just plain weird electrical glitches. If there is one insurmountable problems on 06+ its the TIPM and CAN bus. The auto transmissions and the DMF seem to be much more prone to problems in these trucks. A supplier or engineering spec was changed that just did not enhance the life of the drive train.
The room in any of the 3rd gen quad cabs is superior to 2nd gen quad cab, without a doubt. It is possible for an adult to ride relatively comfortable in the 3rd gens where it was not that great in a 2nd gen. Children and teenagers have no issues and the 4 doors are a big bonus.
Attention: TDR Forum Junkies 
-{}). You get the 5. 9 cummins without early EGR and DPF issues of the 6. 7 (again :-{}).
