I recommend 2005/2006.
Many reasons.
Why 05/06? I'm actually curious since I don't know the answer to that myself. I know 05/06 had the 6 speed which is a big plus. Anything else I'm missing?
Ah hah! Instead of sleeping, I dug this up:
http://www.ebay.com/gds/Jeep-Wrangler-TJ-Model-Changes-By-Year-1996-2006-/10000000004878819/g.html
Lordy!
Note that it doesn't seem to include changes for 2006! 2006 had the dual top option on the unlimited and there was something else too... I can't remember. :-(
98-00 TJs have the port an aftermarket external diagnostic code reader can plug into but they can't self generate the diagnostic codes that display in the odometer on their own. All other model year TJs can generate and display their own diagnostic trouble codes in the odometer by turning the ignition switch on-off-on three times within five seconds.99-00 had no OBDII port?
I'd want something no newer than 2004. 2005—2006 is when the major OPDA (oil pump drive assembly) issue hit the 4.0 engine that can be so hard to fix. And for me personally, it'd be a 2002 or older so I could get the nearly bulletproof 32RH 3-speed automatic transmission. Ideally I'd also skip the 99-00 years where the onboard diagnostics were missing.
The OPDA wasn't that hard to fix. The hardest part was manually turning the crank to get TDC. Other than that it was just slight adjustments on the OPDA itself to get it lined up perfectly.