The 5. 9L gets better fuel efficiency, but I would NOT let that be a deciding factor. The 5. 9L with low mileage and un modified are hard to come by... they do exist, but you will pay dearly for one. Buy one that been modified or high miles and you can find a deal or two. IF I were deciding on a 5. 9l vs. a 3rd gen 6. 7L, I would buy the 6. 7L in a heartbeat. You can get them MUCH cheaper than the 5. 9, since they are newer, you tend to find them with lower miles. Since they are the phase 1 6. 7L engines, they do have somewhat of a stigma about being trouble prone, which will lower the price vs. a comparable 5. 9l equipped truck. Buy the 6. 7L, you get an exhaust brake, if you purchase an auto, you get the 6 sp. auto vs. the 4 sp. auto behind a 5. 9l. Shop around and find pricing on one of the well designed delete kits for the 6. 7l and keep that dollar amount in the back of your mind and just figure on spending that on the truck. The addition of the delete kit will get rid of all the trouble prone emissions crap and get the fuel mileage back to the 5. 9l range, All with 2 extra gears, more power, lower purchase cost... etc... . Just my . 02..... Remember there is not much difference between the trucks... just engine/transmission differences.
Its almost comical sometimes at gas stations... It usually starts with someone looking at the front end then the tail lights and the conservation starts with, "Hey, nice truck, that an 06 model?" yeah. . " Man, pretty clean old truck... how many miles u got on it?" uummmm bout 50K... " U interested in selling it? sure... bout 33K oughta cover it unless I have to put tires on it, these factory ones are gettting lots of weather cracking... . U want it with or without new tires?
Ive only had two that pushed the conversation past there... .