I'm currently in Afghanistan and when I get back to the world I plan on getting a 199X-200X Jeep Cherokee as a BOV.

Other than the obvious, what mods to the vehicle would you do to have something that you could both drive to work and also have it ready to go at a moments notice in an emergency.

I have my loadout already for it, just wondering what mods I should do to the vehicle itself.

Depends on how much $$$ you want to spend and/or how radical you want it to be.
For general purpose I'd think along these lines:
1. Upgrade to mud/snow tires
2. Prepare a H3ll box and keep it in the Jeep. the list of things to go into H3ll box should include at least:
a) extra fluids oil, trans anti-freeze
b) spare set of hoses and belts (I just replace the ones that are on before they need it and keep older ones as spares)
c) tire plug kit & air compressor
d) spare set of fuses and an assortment of electrical connectors with a crimping tool
e) a set of tools
f) jumper cables
g) 2 pairs of gloves 1 cotton and 1 leather
h) a come-along with a set of chains and 20' snatch strap along with a tree saver strap
i) spare set of spark plugs and a rotor
j) duct tape and electical tape
k) bungy cords

Thanks for your service! Our Scout Troop has been sending care packages to guys from Bragg in Tallil, Iraq for a while. They're from the 82nd. We've got some guys we support at Khandihar also, near your part of the world. God bless all of you folks.

As an owner of a Jeep Cherokee that has taken me to the ends of the earth and back without a whimper I can tell you they are very capable from the start. I would say that only minimal modifications can make them billy goats.
1. Mild (2-4 in.) lift.
2. 31X10.50 tires on steel wheels. If you bent a rim you can hammer it back, you can't do that with aluminum. Also spend the money for good tires. I now buy only Goodyear ATXs and have never ruined one. Killed many BFGs in the past though.

4.ARB Air lockers or Good Limited Slips like Power Locks.

Other options if you have the cash:
Lower gears 4.10-1s are perfect especially with 31X10.50s
If auto trans, and external trans cooler
External spare tire/gas can carrier with a handyman jack.
Roof rack