The ULSD used on on highway applications is 15 ppm sulfur content whereas off-road (a.k.a. red or tax-free) diesel has a sulfur content right now of 500 PPM. This will all change in 2010 when the ****** bags at the EPA will require all diesel fuel to be 15 PPM sulfur.
Sulfur is what gives diesel it's lubricating properties (called lubricity) and it's also what gives it the odor. Older engines with fuel-lubricated pumps will be hurt the most since the fuel can no longer lube the pump parts (EPA doesn't care - they think you should buy a new diesel that's compatible with their garbage.) So yes, the off-road diesel is better for your truck. But there's a downside. If you get dipped and are found running off-road diesel you will get a major fine. Usually it's on the order of a few grand fine, plus you have to drain the fuel tank and pay and a penalty of $X per gallon of fuel in the tank.
So basically if you want to risk it that's your call. Me, I just run the on-road crap and add some motor oil or, in the future, used and filtered motor and vegetable oil. This will more than offset the crap ULSD.
As a footnote, I have a farmer friend who brews his own biodiesel in his 24-valve Cummins. He told me this weekend that with straight ULSD the truck bucks and snorts and generally runs like crap. Running B80 the truck runs smooth as can be.