Wheeling rig, expedition rig, or just a daily driver?
Changes through the years can be found here:
http://wjjeeps.com/newoptions.htm
I'm partial to the 2003 for the side air bags and the LATCH seat anchors in the back.
2004 (last year) for the 7 slot grille that don't follow the lines of the front end (ugh).
There were supposed to have been some AirCon issues in the 99-01s. Something about a badly soldered circuit board behind the dash (controller) or expanding/exploding capacitors or something. These issues can be fixed (DIY) or later WJs don't have the problems.
There's three engines: 4.0, 4.7, 4.7HO.
4.7 has more power than the 4.0 and gets the same mileage according to EPA (fueleconomy.gov). That's what I'd get. The HO takes premium fuel IIRC.
4.7 seems to have a good reputation. It is a modern engine design with SOHC and designed to be efficient (for a V8). It'd take it over the 5.2/318 in the ZJ any day.
2002 up will have the Akebono front calipers instead of the Teves-Continental ones. The Contis are prone to warping.
http://wjjeeps.com/brakes.htm
Again, something that can be fixed if you ever encounter the problem.
IMO the case to get is Select-Trac (NV242). It's all mechanical and no electronics or viscous couples to go bad. Only seems available with Laredo and Limited trim levels with 4.0 and 4.7. You can tell whether it has SelectTrac or not by looking a tthe bezel on the shifter. If there is no 2WD mode then it is not Select-Trac.
I think that's the biggest stuff... Generally seem to be good value and I haven't heard a lot of negative about them. It's the last of the low tech, non-Wrangler Jeeps. Chryco went retarded and started putting electronics in the transfer case (among other places) of all the station wagon Jeeps after this.