Regearing is the best option.
The problem with the 3.8 is it was pushed to it limited for the most part to begin with. So gaining HP out of the motor can only be achieved by adding a supercharger. The intake is not restrictive so adding a CAI does little to nothing. A larger viper throttle body only causes thrown codes and in some rare cases puts the vehicle in limp mode. Even the exhaust isn't very restrictive and a Cat back does little if your not replacing headers back. The Tuners help throttle response but little in hp gains. And if you did it all, it would be nearly as costly as a Supercharger which gives real gains. One place did a dyno once after adding a CAI, Headers and exhaust with a tuner running and all they got was 10hp gains and that was at max RPM's. At driving RPM's it was more like 2 to 3 hp.
Saying all that, Their is better hp in the 3.8, but it is at higher RPM's. The problem is at normal driving speeds/RPM's there just isn't any hp or torque. That is why many re-gear. The JK was just under geared for the 3.8 motor and especially the Automatic transmission. So by regearing, it puts the motor in it's optimal RPM to hp band. Regearing just does wonders for the pre 2012 JK's.