3.7L automatic, Command-Trac.
Auto - 'cause though I'm a lifelong stick-shifter, I have enjoyed the several automatics I've owned, and the auto Libs were pretty much what the dealiers had, except for the Renegade, which had lots of stuff (and price) that I didn't want. I haven't had occasion to regret the auto yet -- the 3.7's got plenty of "scoot" to push it, and I still can manually control the shifting with the overdrive lockout button and the auto shift lever.
Command-Trac (part-time 4wd) 'cause I've read it's much tougher/sturdier than the Selec-Trac. I believe the Command-Trac is the same system that's been on the original 4x4 Cherokees "forever." Very tried-and-true drive train, and I've been told that it gets better traction in seriously-bad terrain. All in all, I've driven Ford and Mazda "part time" 4wd systems for years, and am very used to the "dry pavement" restrictions of those systems.
Also: I do some towing from time to time, and the Jeep automatic is rated at a higher towing weight than the manual. Usually an automatic is suggested for towing systems because of the need to slip the manual's clutch under heavy load, which often results in faster wear on clutch and ****** parts (on the manual ******.) I'm pretty good with a clutch, and haven't had that problem, but an automatic is certainly a bit easier on the entire drive train than is a manual.
I'd be glad to have either one, but when I'm driving to work (or in the mountains) with a cup of coffee in one hand, not having to de-cup to shift is really handy...