I hear a lot of good things about 1999 - and I heard about them AFTER I got my 1999, so it is a little less biased:roll:. The ones with 8.25's are 29 spline (along with 97, 98, and some 96's), there is no risk of vacuum disconnects, the 4.0 is likely to have less mileage (just because of it's age), and it has more unibody reinforcement than earlier models.
Most of these advantages are off-road perks, though. The drivetrain on XJ's varied very little throughout production, so you will likely be in a similar boat regardless of year chosen. Naturally, I would still lean toward as 'new' as possible and/or as few miles as possible. If you are looking for longevity, the way it has been treated by previous owners will have a lot to do with the rest of it's life. If you can find one that has been a grocery getter with all the previous maintenence records in the glove box, you'll be best off (as with any vehicle purchase). The drivetrain on XJ's is pretty solid and able to withstand lots and lots of miles. If the 4.0 is taken care of, it lasts a long dang time...as you know. Out of curiosity, what happened in the 2000-2001 production years that steers you away from them? The change in the fuel injection system? A lot of guys here just don't like the front axle, but it is an off-road concern.
Good luck!