OK here's a few;
If you have replaced the steering wheel on your CJ use the turn signal bright/dim switch for the front air locker (those with newer vehicles can put a dimmer switch on the floor and use it for either the air locker or to dim the head lights.
Mount an ammo can under the hood for tools (they cannot steal what they do not see).
Use hose clamps to keep extra radiator/heater hoses attached to the grill support bars (Use the straight universal fit radiator hoses).
Use the existing rear spring mount bolt locations with longer bolts to mount your rear CJ tow hooks, hook pointed up (cut the tips off of the hooks so that you can get the tow straps over them).
Use Velcro "One Wrap" (double sided Velcro) to secure things like flash lights, folding saws fire extinguishers etc. to the roll bar.
Hide a switch to run the winch from inside the vehicle up under the dash to keep curious fingers to from activating it.
Mount one of a pair of stereo speakers above the mirror on the windshield frame then run the wire inside the frame to the CB radio (makes it much easier to hear what is going on) (CB radios are cheap and make communicating within a group much more interesting on trail rides).
One wrap (Velcro) a can of bear spray to the seat frame so that you can get to it easily if large dogs are encountered when trail riding with the doors off (did this after an encounter with great danes). (I asked the local LEOs at the cop shop and they said that pepper spray is not considered a concealed weapon in Colorado, check local legalities before you do this.)
Use a box end wrench to compress the fingers on E-brake cables so that they can be removed from the backing plate.
Use a length of 2" PVC pipe with end caps to store your welding rod for off road use (Cheap & water proof) (One wrap it to the seat frame.)
Check your dash for unused indicator (idiot) lights (YJs and newer); activate them and use them to indicate air lockers, rock light etc. activation.
Use a scrap yard 80 amp or larger alternator to help keep from killing your battery due to winching (or excessive numbers of lights/stereo amps etc).
...a well prepped, well driven, vehicle should do well in any terrain, including the highway.
Carburetors became obsolete during the last century... do what ever it takes to get fuel injection...It makes bigger grins off road.