I am thinking of getting a Jeep TJ. Any one have good, or bad comments on them? Gas mileage? 4.0L standard...?

The mileage is terrible on the 4.0, but not that much better on the 2.5, so its not that much of a trade off, I'd def. get the 4.0. Do not forget about insurance, that is not cheap either.
If u plan on doing a lot of off road driving in rocks & other situations where u will need to drive 2 footed u should get an auto transmission, but if it is going to be mostly a road vehicle the manual will get u better mileage & u can add a hand throttle for the occasional 2 foot situation.
Try to get one with a Dana44 rear axle if u can. The diff cover is sort of stop sign shaped as opposed to the D35c which is oval shaped - its a much stronger axle. They were optional on the Sport & Sahara models, & the later model X is & the special edition Golden Eagles & Rocky Mountain Editions. Standard on a Rubicon as well (along with a TON of other stuff that makes the Rubicon a much more capable off-roader, & for this reason, more expensive). Try to find gears that r 3.73:1 or 4:11 (Rubicon). This will save some of the low end power u lose from adding bigger tires. The gear ratio is stamped on a little tab attached to the differential housing.
If u can find one with dual tops u should consider it. You will want the hard top if u live where its cold, if u do not want it u can sell it on CraigsList for anywhere from $800 to $1000 depending on what time of year it is (you will get more for it in the winter)

we had a 03 4.0 auto and it got ok mpg it had 31in tires. l would get a manual it will help out with the mpg plus the auto is are junk

be careful with the 1999 models.there has been alot of trouble with them.wranglers and cherokees alike.you have to have the 4.0.with a manual transmission.