I like all of my mods... in no particular order, other than how my brain happened to recall them:
Bypassing the failed fog light switch on the multi-switch to a factory-matched switch in the dash.
Upgrading to the double-din radio (and amp, sub, speakers).
Upgrading the front seats to JK.
Full carpet kit.
LED headlights w/ DTRL.
Upgraded the factory fog lights with LED bulbs to match the color of the headlights.
Dash/console lighting upgraded to blue LED.
Wet Okole seat covers w/ heat & lumbar.
New Rough Country 2.5" suspension kit, along w/ new wheels and 32" BFG K02's (rides great now!)
3rd brake light inside spare tire.
Flipped mirror.
Swapped visors.
Indexed window crank handles.
Made phone mounts that are secure and don't interfere with factory stuff.
Foot pegs for when the doors are off.
Aux mirror mounts for when doors are off.
Added eye-bolts to the holes around the tub lip for securing bungee cords, cargo net, etc. (helps keep my shit in the Jeep).
Aftermarket TPMS system (to hopefully catch any small leaks).
Brush guards on all of the lights.
Other shit is just maintenance and/or repair, but still worthwhile and necessary to enjoy the Jeep.
The wife will say none of these things thrilled her as much as when we finally got all of the John Bull East pinstripes buffed out!