Most of the mods I didn't end up liking were on my old Bronco:
-Rancho 9000 Shocks (with factory dual shocks up front): Way stiff, even on the low settings. Also, the finish was thin and they rusted.
-BFG M/T tires: Nice off-road, but made a loud truck even louder on the highway. In the desert, the more aggressive tread didn't see much use.
-Sound proofing with a roll of "Ice Guard" material. The truck smelled like tar for a long time, and it ended up trapping sludgy water under the carpet
-Ripping out all of the carpet and going with Herculiner - While this made the truck hose out, it was LOUD. I really should have put another carpet kit in. Also, bed liner surface traps dust and is hard to clean unless you pressure wash it.
-Sun roof: Installed by previous owner. Always leaked and made noise on the highway.
-Tailgate-mounted spare tire. Only go with a solution that mounts to the frame. I ended up with a 4" crack in the sheetmetal.
Things I liked on that truck:
-33x12.50 tires on a full-size truck with a V8. This is a good size for a larger truck used in the desert
-Detroit Locker: I actually like them on a full-size vehicle. You have to be careful on turns, and you can break things much more easily if you have lots of torque.
-Manual transmission with a very low first gear - I rarely needed 4-Low with that 6.67:1 gear available on the shifter.
On my new truck (Toyota T100), I did a few things differently:
-Bilstein HD shocks (love them)
-Goodyear Silent Armor Tires (very quiet on the highway, wear well, good in dry climate off-roading)
-Eaton Gear True Trac rear diff (Rides like a more aggressive limited slip, no need to think about it)
-Automatic transmission (Good for taking off in soft sand/etc, easy to drive in Winter)
-Buying a quiet, easy-to-drive vehicle in the first place. Now my wife isn't terrified to drive!
-6.5' Bed that I can actually sleep in. The Bronco had surprisingly little usable room for its size - lots of things sticking out, floor at 3 levels, etc.
Arclight