The best mods to do really depend on what you want to be able to accomplish...and your budget and time frame.
How much $ over what time do you want to spend?
What kind of terrain do you want to be able to beat?
Examples - (General, plenty of variables)
For rocks, you need armor, like rock rails and skid plates to fend of rock rashes and help prevent you from trailing pools of oil, gas, body shop receipts, etc...
For slow crawling over boulders, alot of wheel travel, alot of ground clearance, low crawling gears, lockers, MTRs or other good rock tire, etc...
For hill climbs, you want to stay low, keep the weight as low as possible, maybe more in front than in back, etc.
For mud, you want the fattest tallest paddle wheel tires you can fit to get flotation/avoid getting stuck....and not MTRs like for rocks, because MTRs are not the best mud tire....Interco Boggers for example would blow them away in a mud hole.
If you do get stuck, do you want to have a winch?
If you need a winch, you need a winch bumper to mount it on.
If your tires are too big to fit under the truck anymore (>31-32's), you need to carry the spare inside (Spare the cargo space?), on the roof (Weight up top, and the clearance issues...), or get a carrier bumper for the back, etc.
Do you need to drive it to work everyday too? Highway, back roads? How hardcore are you able to go w/o messing it up as a daily driver for you? (The tire choices make a huge difference here...)
Deep water crossings in your future? Might want a snorkle, etc.
Do you have to park in a parking garage? If you do, that limits the height a bit...I have a 3" SL+2" BL+33's....and I can't get into most garages in NYC...the ceiling signs go BANG! BANG! BANG! as I try to get in, and then theymake me try somewhere else, etc.
Your own garage if relevent may also be an issue, etc.
In short...
You have to think about an upgrade path that realistically reflects the time and energy you are willing to put into this hobby....
And THEN start modding.
Unless you meant you were wondering which smiley ball to put on your antenna to help find your X in the mall parking lot...
(You can off course do any of the above stock....its just how far you want to increase your capabilities....there's no wrong answer)