I have had 4 tjs (1997,1998,1997,2003) so my knowledge is based on those. 1997s are solid and good trucks but a few small things that are unique to them (wiper cowling and ac controls). They are known to have some small issues with the clockspring in the steering wheel as well as the ac controls going a little haywire. 1998-1999 are great and IMO the best early years, and a big plus is that they have the ax15 5-speed which was swapped out in 2000 to the NV3550. The ax-15 is a little cheaper to fix and has less issues from imo. They NVs don't like to shift when they get a ton of miles. 2000 get the NV3550 and coil packs so thats a nice update but the distributor worked fine in all my jeeps so to me its nether a plus or minus. The 2000 and 2001 ones are known to have head warping issues depending on a casting number so that is something to look for. 2002 as far as I know is the same as 2000-01 but without the head issues so they are a solid jeep. In 2003 they updated the interiors and IMO made them much nicer (better seats, gauges, steering wheel, windshield trim, ect). As far as I know 2003 has no issues and the same goes for 2004. In 2005 they swapped to a new computer and a 6 speed both which have proven to be less reliable than the previous years. The 6 speeds are expensive to fix because they are Mercedes sourced and they have similar issues as the NV3550 when they get some mileage on them. The other issue with the 05-06 is the OPDA issues they have because of the new computer. They changed the distributor to convert it to fire the new coils and sometimes they fail and cause camshaft failure, just do a search for jeep tj OPDA failure. That's the basics of them as far as I know, but they are all pretty solid, most issues are nothing major but some things you need to look for.
As far as 2007-2013 go, I believe the early ones (2007-2008) have oil ring issues and they can use oil, however I have never owned one to vouch for this. Also in 2012 some of the early ones had lifter issues I believe.
TJ-Solid jeeps, not as comfy as the newer ones but they are brick ****houses, I love my TJs.
1997-First model year w/ some unique parts. Watch out for wacky ac controls and airbags lights.
1998-Solid Jeeps, nothing year specific I know of
1999-Same as 1998 no issues I know of
2000-New trans is a downgrade IMO and watch for head issues
2001-Same as 2000 depending on casting number
2002-No issues I know of but if you can afford an 02 IMO an 03 is a much nicer jeep because of the updates
2003-Solid with no specific issues I know of
2004-Same as 2003
2005-6 speed IMO is a downgrade and watch for OPDA failures
2006-Same issues as 2005
Jk- New jeep with lots of good aspects but IMO the 3.8 motors are not to great
2009-No issues I know of
2010-No issues I know of
2012-New motor (improvement over the 3.8) but early ones have lifter issues (covered under warranty)
2013-No issues I know of
WTB INCA GOLD HALF DOORS PM ME
2003 INCA GOLD TJ Rubicon 5 speed 3inch Currie/Savvy Lift, JKS Discos, 305 KM2s
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1994 Grand Cherokee 5 SPEED 3inch lift, tj bumper, 31x10.5s, wheel spacers, rhino liner, ect.....
1998 TJ Sport 5 Speed 31x10.5s, completely murdered out, and a short throw haha (miss that jeep)
1999 TJ SE 5 Speed (ls swap that became a part-out due to excess frame rot)