I have had/have 5 third gen trucks now. My '03 HO's were awesome trucks, best milage of the bunch. I breifly had an '05 and now have an '06 Megacab and an '03 2500 QC Hemi. All have been 4x4 autos and all have been completely stock engine wise.
Certainly the loaded up Mega is my favorite. The power moonroof, rear DVD, power sliding rear window, Sirius radio, factory jake brake, high idle control, and slight power advantage over the 305/555 trucks all make it my favorite, but for a higher price of course.
I greatly prefer the 48re auto trans. If all I did was heavy hauling for a living maybe I would go manual but the autos are so much better for daily use, and are much faster too. I have seen 22-24mpg with the '03 QC SB 3. 73 gears, and the truck was great. I am getting 20-21mpg with a well broken in Megacab that scales at 7700lbs empty. once broken in they all do well for mpg. By comparison, in the same type of driving, the Hemi gets 15-16 mpg empty.
I do think that you will have trouble finding a $20k diesel third gen. I have been looking myself for an '03-'04 and they are much closer to $30k than $20k. I am glad I have an '06 though. I hate the stupid bubble tailights the '07s have, and I think the 6. 7, while a fine machine is way too complex in the emissions dept. Looking at the exhaust system alone scares me. Any third gen that has been cared for is a good bet IMO.