I was in your place back in 2006, and though a lot has changed since then, the big three build trucks under the same principles. I test drove over a dozen trucks in all, from all three makers, and all were diesel, with automatics. A lot of that selection has to do with what you want to do with the truck, and what is a priority to you with features on these trucks. You have this posted in the DRW section, so I'm going to assume you're looking for a 1-ton truck or better with DRW's. This is my experiance with my search, and the truck I purchased (in sig) and I still drive.
If you're looking at comfort of ride over anything else, hard to beat the smooth ride of GM. At the time these were the most horsepower trucks on the road, what crippled it was the 3.73 gears in the axles. The frames were not as strong as the Ford's, and the IFS on these trucks will lead to issues down the road.
Dodge's biggest claim to fame is the Cummins under the hood, the straight 6 will always be more reliable to a similar designed V8. The transmissions on these trucks are a major issue, particularly the automatics, and the frames are the weakest. The cabs were smaller back in '06, with the exception of that huge MegaCab. I did test drive one, and struck it from the options. The 8ft bed wasn't an option, and the extra length in the cab is all steel, which makes for a huge blind spot.
These trucks are built for the working man. If you count the number of commercially driven trucks in your area, I'm willing to bet the Ford will out number the other 2 combined. The transmissions are great on the '03 and up trucks, and the frames last longer. These trucks use heavier axles and springs. Each of the motors have an issue, but the aftermarket has responded and they can be made bullet-proof. As for the interiors, hard to beat the comfort of a fully furnished King Ranch. Me, I prefer the cloth and simplicity of the XLT. Ford's are the heavier working trucks, even the massive towing capacity of the '08 and up F450. My '07 F350 with the TowBoss package is effectively the fore-runner of that truck. Each truck is going to have its flaws, and possible repairs. You want a truck to last a number of years get the Ford.
My rig is my daily driver, with around 70k on the clock. I've learned more about it in the last few months, because I neglected its oil-cooler issue. I'm working toward getting the 6.0L bullet-proof in my truck, and I'll bet she'll still be strong after 300k or more.