Depending on the amount of dough you're willing to spend there are a bunch of options.
1. Weber carb 32/36 is $380 or so.
not that much of a power gain, but much better reliability and simplicity under the hood.
2. Ignition upgrades. Driveajeep.com sells a great upgrade for the stock distributor cap. It replaces the old cap with one from a F-150. I don't have this upgrade, but I've heard great things about it.
I don't know anyone who has done a new ignition box, but I bet you could find one if you looked around.
-Also go to this sight for 10 free Hp. www.outdoorwire/4x4/jeep/tech/electrical/jn-ignition99/
I did this upgrade and its really easy and cool.
3. There are other basic things you can do, such as new cam, valves, springs. Headers and Intake manifolds too. All this stuff can be found at Cliffordperformance.com
4. Another upgrade that more and more people are doing is the 4.0L head swap. This head has much better flow than the 4.2 and its pretty much bolt on. There's a good write up at http://monsterslayer.com/jeep/40Head/40Head.htm
They claim its a 40 Hp increase.
There are other upgrades I'm sure, but I can't think of them off the top of my head. Email me at email@example.com if you want more info.