X2, the 4-speed AW4 from a Cherokee is a very popular swap for the TJ. It's not a bolt-in swap but neither is it that difficult as shown in the above link from Jeepsr4m. I helped install one into a TJ that competed in the King of the Hammers event last year, it's that good of a transmission.
The easy bolt-in automatic tranny swap is the 32RH 3-speed auto out of a '97 to '02 TJ with the 4.0L. I did that swap two years ago and it can be done in a weekend.