That's a very general open-ended question! A lot depends on what your Jeep will be used for and how mechanically adept you are
...but here's my .02...
-remove traction bars and sway bars for MUCH better flex, I drive mine daily and can't say that there's that much difference on road
-Herculine the interior (should cost under $100 US, relatively cheap...makes a world of difference
-make a home-made snorkel (black PVC pipe) should cost approx $50 US, may not look as pretty as the $300 jobs but it will work, there's plenty of write-ups on this forum and on the web
-have a hi-lift jack? install a mounting system on the back roll bars using a couple of fence post clamps, works great
-keep browsing the YJ/General Offroading/Cheap Fixes sections of this forum...you'll find plenty of other ideas
<'93 YJ, 4.0, 4" Skyjacker lift, Rancho shocks, 33" BFG A/T, 1 1/4" Greasable shackles, Herc'd interior, Herc'd full hard doors, track/sway bar delete>