I bought my 2000 Wrangler in March 2010. It had 31inch AT's but was otherwise pretty much stock. There was also a soft top under the hard top still in the factory configuration.
I'm pretty sure it had never seen so much as a gravel road in it's life. The guy I bought it from was the second owner and he had pulled it behind his camper for years. Once I started off roading it, I realized there were some upgrades that I needed to make.
So far I have pulled the milk jugs off of the bumpers, painted the fender flares, added a Teraflex cb antenna mount, Champion Winch, Trail Gear rock sliders, 33x12.50 Goodyear MT/R's, and a 2 inch Rough Country budget boost with shocks.
I've also added a Solid front differential cover, Raingler grab handles, and a really sweet front grille guard/winch mount. I've ordered and installed an in cab winch control kit that I plan on doing a write up for with pics.
Update 8-2011: I ordered a Ford 8.8 rear axle from ECGS and had it installed at Rock Your 4x4 by Jason Cooper. That netted me a much improved rear axle and as a bonus an extra half inch or so of clearance in the rear. My next upgrade is going to be 3 inch front springs to give me clearance up front and a more level ride.
Update 11-2012: Last spring I changed my front springs out to 3 inch springs from Rusty's Offroad. Then after bending my transfer case output shaft on trail 54b, I had Joey at Atomic City 4x4 install a SYE kit. Good times!