Since were speaking of mods not to avoid heres my thoughts
1. cooling system upgrades
a. heavy duty rad
b. convert closed sys to open sys (older models)
c. vents or raised rear hood
d. zj fan clutch
e.Elec fan override
2. steering mods
a. steering box brace
b. zj v8 tie rod / drag link set up
c. smaller pully on pump (genrite)
3.armour
a. front and rear bumpers w/ tow points
b. winch
c. fold rear quarter panels
d.sliders or nerf bars
e.diff covers stronger than stock not chrome or aluminum
4. suspension
a. lift of your choice
b. upgraded shocks w/bar pin eliminaters
c. proper size tires based on lift and wheeling
5.upgrade sterio system
6.trans shift kit / allows use of all gears individually and allows youto be able to shift your auto trans
7.Fire extinquisher and first aid kit PRICELESS !!!!
8. Some type of comunication system other than a cell phone.
9. Boony kit .... back up supplies for trips into the wilderness, blanket,food, water, toilet paper, heat source (a metal coffee can with a roll of TP in it , pour a little alcohol from first aid kit on the TP , it will burn for hours , safe and will heat up a jeep interior) Basically anything you think you might need if you break down and can't get home to keep you and your family alive.
10. recovery kit with a tire plug kit in it I use the trail gear kit cheap and it works well

The last two you may not consider a mod but being safe and keeping your passengers safe and doing all you can to have a great time and still get home is a mod you can't ignor in my book .

11. axle upgrades
a. gear ratio to match tire size
b. high pinion 30 frt chrome molly axles w/ over size u joints
c. anything but a 35
d. traction control device if you have the need
12. accessories?
a. high lift jack
b.axe/shovel
c. air compressor or on board air
d. secure way to mount it all
Yes the list is long but everything here in my opinion is a mod not to avoid if your gonna wheel it. As Steve said alot of this would be based upon demografics, money, and ability. Which is why this fourm is so important , if you cant do it or haven't I'm sure somebody here has and more than likely would be willing to help you do it.