Here is what I think is a great summary that I found on this forum some time ago when I was looking for a used vehicle. I take no credit for the content, but can't give credit where credit is due because I don't remember who the original author was... I just kept the info for reference. So having said that, here ya go...
Best - 2006 - 2007 Chevy/GMC 6.6L Duramax. 2008 on up have extra emissions equipment that will lower mpg but are also excellent engines and transmissions with a lot less diesel exhaust smell. 3/4 ton 2500 vs 1 ton 3500 single rear wheel axle models only differ in an extra leaf in the rear spring pack on the 3500. Otherwise the frames, drivetrain, axles, gearing, cabs and everything else is identical. 2005 and prior Duramaxes have 5 speed Allison transmissions instead of the 6 speed Allison in the newer models and the engines were a bit more problematic. Early Duramaxes 2003 and prior were known for Fuel Injector problems. 04 and 05 models may have overheating issues when towing very heavy loads. In 2006 Chevy made a number of design changes to beef up their already excellent Duramax diesels and made them considerably more powerful/torquey as well as adding the 6th gear to the transmission.
Better - 1999 - 2003 Ford 7.3L Powerstroke. Work horses! The transmissions on these are not as tough as the Chevy Duramax Allison transmissions. If you buy a higher mileage used 7.3 powerstroke plan on a transmission rebuild. Get a quality transmission rebuild with towing parts and the transmissions can be made pretty much bullet Proof.
Better - 2003 - 2004 Dodge 5.9L Cummins. These are inline 6 cylinder engines opposed to the Ford and Chevy V8 cylinder Diesels. Less parts = less to go wrong. Excellent power potential on these engines and probably the best most rugged engine ever put in a Pickup. The Cummins 5.9l is simply a legendary diesel! Like the Ford 7.3's plan on rebuilding the transmissions on higher mileage trucks.
Old but excellent - 1996 - 1998 Dodge Cummins. Similar engine to the 2003 - 2004 Cummins but less refined. These are mechanically injected engines versus the newer electronically injected engines. The simplicity of these engines are prefered by many. As with the Ford and newer Dodges plan on a transmission rebuild when the miles get up there.
Wimpy - GM 6.2 Diesel engines. Only slightly better are the GM 6.5 Diesel engines. Neither are very efficient or powerful engines. Thank god GM did not design the Duramax engines... they got Isuzu to do that for them. With the debut of the Duramaxes GM went from the bottom of the gutter up to the top of the heap while Ford was going from a great Diesel engine (designed by International) to one of the worst Diesel engines.
Worst - Ford 6.0L Powerstroke diesels. Lots of problems! I found many older 7.3L Powerstroke diesels commanding higher prices than comparable mileage 6.0L Fords. I had intended to buy a 7.3L Powerstroke but found that they command such a premium price that a Duramax was a better choice for me.
In 2008 new EPA regulations restricted the pollutants that diesel engines could emit. All manufacturers had to make changes to their engines to accommodate these regulations. Every manufacturer added diesel particulate filters (DPF's) to the exhaust paths of their engines. These DPF's build up the unburnt particles in the diesel exhaust and plug up. The engine control routinely burns off these particles by injecting diesel fuel or Urea into the DPF to raise the temperature in the DPF and burn up the trapped particles. This cleansing process either burns diesel and lowers mpg or Urea which has to be replenished periodically. This is comparable to the mandate of catalytic converters in the 70's. Eventually DPF's will be improved and be more efficient resulting in less effect on the performance of the engine.
I recently purchased a 2006 Chevy Duramax 2500HD crew cab long bed and love it. If I ever need the extra payload capacity of a 1 ton I will add air bags which will give me the payload capacity of a 3500 with the unloaded ride of the 2500. I test drove a 3500 dually and the streets were suddenly very small and very narrow. If I could have made do with a short bed I would have been all over a Dodge Mega Cab with the legendary 5.9 Cummins engine to get the expansive cab with all the extra rear seat room.
Some good reading: http://www.dieselpowermag.com/features/1........_10_best_used_diesel_trucks/viewall.html
P.S. The suggestion to plan on rebuilding transmissions are based on Automatic transmissions. Manual transmissions are usually less prone to internal wear and problems and generally only require periodic clutch replacement.
*Disclaimer: These are just my humble opinions!