You know that's almost an open ended request. Anything that moves , turns, or flexes should be checked. But to be just a little more specific here's what I went over on my "new" 05 I got a couple of months ago.
Plugs, belts, coolant (flush and refill with 50/50 mix), diff lube, X-fer case lube, tranny fluid and filter (mine is an auto), air filter, shocks and steering stabilizer, radiator hoses, thermostat, fuel filter, oil and oil filter. (Also replaced heater control panel, speed resistor and fan blower motor but that was really more of a repair.)
Pulled both drive shafts and checked u-joints (looked for dry or stiff movement as well as too loose), checked front axle ball joints (no play), checked axle u-joints , checked the brake fluid (probably should flush and replace), checked brake pad and shoe wear as well as rotor thickness and drum wear, adjusted rear shoes (had one side kinda loose), checked bottom of water pump for any leakage, had front end alignment checked, pulled the skid plate and checked the tranny mount...(cleaned and coated the skid pan with truck bed liner), this list can go on forever but you probably get the idea by now...
The basic idea is to give your jeep a serious eyeball and address annoyances now before they become a trail breakdown later..