Wow! ok I'll start with the Ford 6.0 just doing the egr delete isn't the answer for the 6.0 blues trust me on that, that engine was built with a bad oil cooler ALL OF THEM! some just go before others, there's no if just when. The 2nd bad thing is the egr then the head studs. The egr and the oil cooler are week and one will crack then the other then the head gasket will blow.we had a 07 it was a nice truck but oh my God living in that fear sucked, also I don't have any good to say about the injectors.
The 7.3 Ford is good but they are getting old now and harder to find with low miles, they are holding in price very well you can not go wrong.
The Chevys diesels
I haven't worked on much just the ones from back in the 90's
From what I have read about them and I would own with the LBZ that is the 06-07 2007.5 GM made some changes the egr stuff and they don't get as good mpg as the older ones I know two people that live near by that have 01's and they get good mpg and they have not had any injector problems but we almost got an 03 that was at the dealership in town but it's a small town and I found out the guy that traded it in had some injector problems so I stayed away from it. like some have already said if you want the 6 speed auto trans with out the egr/dpf crud get the lbz if you can find one but know before hand that Chevys cost a little to fix.
Dodge 5.9 I have heard that the 2006 did not come with the 6 speed auto trans and we went with an 08 6.7 6 speed auto trans with a Jake brake the paint on Dodges doesn't hold up as well as the others (Ford & Chevy)but hey I live in MN. So if a person drives in the winter the truck is going to rust, we keep ours parked in the winter, someone on page one said that the dpf and egr stuff isn't a huge issue well no it's not if you only do freeway driving the newer trucks go into regen mode and you have to drive 45 mph fro like 15 to 20 min and it has to finish it's regen if you don't let it your truck will have a code on the over head and if you don't get it taken care of your truck will go in limp mod also you have to have the dpf system cleaned as part of regular service... We are running a tuner on our 6.7 on econO tune (that's not hulling anything)at 55 to 60 mph we get 25 to 27 mpg 14 to 16 in town not going by the over head with the TT in tow the TT is about 8,000lb loaded 11.5 to as good as with the wind at our back 15.9 that was driving at 55 to 58 mph but most of the time towing we are getting 11.5 to 13 mpg we had a Dodge 4.7 gasser when we had our other TT 6200lbs 9 to 6 mpg. I went with a Dodge because they are easer to work on I worked in the field on Cats for 20+ years and I know a little about diesels and some people are saying that the egr and dpf systems are falling off their trucks at high speeds. The dpf and egr systems on all the newer trucks are the worst thing that has happened to the diesel trucks they will plug-up sooner or later, they will all get good mpg till they start plugging-up.
If I had to do the truck thing again I would have keep the Ford I would have pulled the 6.0 (it had 90,000 miles on) and sold it and then put a 5.9 or 6.7 Cummins in it the ford was a better riding truck