If you're going to V8 a 2006 TJ, the logical choice is a 5.7L HEMI swap. Native electronics makes it easier to use than the older 5.2/5.9L Magnum V8, federal and 50 state emissions legal as well. The golden rule on engine swaps is equal-to or newer than the vehicle it is going in along with same weight class as the donor. That is a light duty 1/2 ton pickup, SUV or a passenger car as the donor, not a heavy duty truck. The emissions controls and ECM are similar in the early HEMI V8 Chrysler products to a 2005-2006 TJ so that makes sense to do. The Magnum V8 was discontinued in early 2003 so it isn't even really a contender for swapping in late model TJ Wranglers. Best save the Magnums for pre 2003 TJ's. Although I agree "technically" the best V8 made is a GM gen 3 and up, it's more electrically complicated to integrate into the TJ and there are some hidden costs there not discussed in this thread such as gauges etc. I have swapped GM Gen 3+ power into Jeeps but always reserved for earlier models due to simplicity sake like the CJ-7's, 8's, YJ Wranglers pre OBD 1 that are pre 1992 electronic gauges etc. I have had very good luck with them, I just wouldn't do it in a TJ without understanding the full changes required and keeping in mind federal government emissions laws. This even if there is no testing in your region of the country should you want to sell or move sometime in the future.
RR