PEAK PUTTERS

So... my 4.0L engine (2006) is absolutely stock and I'm wondering if you all have found any truly worthwhile mods to improve its performance. I've read that header and exhaust mods realize very little effect... and that most "chip" improvements aren't worth their cost. What have you found useful??? Thanks!

Gears. You already have those! I have also read all the reviews on headers and CAI kits not gaining any power or mileage on our modern 4.0 engines. The stock air box is not restrictive and provides the best protection against particles getting in the intake.
Supercharger/blower is one of the only ways I have read to get substantial gains on our motors.
Our friend Pat from the D-Rats has one on his TJ. He likes it so much he is installing another one on his built up TJ Rubicon he recently bought. He will be at PUAM. Hopefully it is done, and he will have it there for us to drool over.
Here is the one on his street friendly TJ. Note that he is using the stock air box. The new supercharger is a different brand than this one.

The thing about a 4.0 is that if you do nothing to it except maintain it properly, it will last forever.

That said, there are some really cool forced induction kits out there that aren't as expensive as they used to be.

http://www.magnumpowers.com/jeep%20wrangler.htm

The one on the photo above looks like an Avenger SC. This link is to a guy in Portland doing something similar...

Honestly, the only real gains will be from ridiculous head mods, major displacement increase, or forced induction. Many die-hards out there disagree, the Jeep inline heads have terrible port profiles and heavy pushrod valvetrains that dont take well to "proper" performance-oriented cam profiles. Forced induction is by far the easiest way to get more power.