HPTuners supports ALL TJs. I use Syked software for my tuning my 2004, but Syked does not have as much community support. I have considered going to HPT, but I'm slowly learning more about Syked.
It's only recently that HPTuners started supporting all TJs. It used to be they only supported 05-06 models, but within the past year (I think it was the past year) they started supporting 97-06, thank goodness.