Some more info on what you plan to do with the truck will help as well. Looking for a tow vehicle, looking to offroad, just looking for a 4x4 truck in general for commuting and driving?
We can start with your year range listed. 2006 is no different than 2005 with the exception of early model year 05's may have had the solid rear diff cover instead of the finned cover. This caused some failures due to high heat.
2007 MY(model year) bumped the HP with a different intake manifold, VVT, and a better flowing exhaust(dual in single out instead of a Y pipe and single in/out muffler).
2008 they addressed the brakes and the rear end I believe. The only problem with 2008+ MY is the fact that you can't get true trac(limited slip) for it. otherwise, to me, it's the best MY of the three. Bigger brakes, same 07 improvements on the engine.
If you're towing a decent amount of weight, you would want the big tow package. This bumps you from 2.94 gears to 3.36. Also gives you extendable mirrors. Problem with big tow is regular highway driving while not towing and fuel mileage. there are pros and cons for BT vs. non big tow so it depends on what you will be doing. BT = You need it for heavy loads, it's faster out of the hole with the bigger gears, I like the mirrors better. It will suck much more gas at higher cruising speeds when not towing. Non-BT = will cruise at highway speeds with low rpms. it can still tow a decent amount of weight with no problems. No big mirrors and maybe no trans temp gauge on the dash(not sure when they added it to all vehicles. For MY2005, if you didn't have BT, you didn't have a trans temp gauge in your dash)
Hope this helps. sorry for rambling.