This is easily the smartest and funniest episode of South Park that they've ever done. Taking on a subject like Scientology is nearly impossible for most because of the litigious nature of the group but thanks to the fast production of the show there wasn't time for Scientology to stop them doing it and we're lucky they didn't.
There are 2 big plots to this episode, the one that a lot of people love is the "Tom Cruise won't come out of the closet" section which is hilariously silly. Throwing in John Travolta and R. Kelly into this story just makes it funnier, R. Kelly's singing to Tom and John to the tune of his rap soap opera Trapped In The Closet is a stroke of genius.
The second plot however is the one that I love most, the part that caused a lot of controversy and led to Issac Hayes leaving the show... going after Scientology. South Park seems to be funniest when it tackles either religion or a current political event and this is the best example. One of the funniest moments is something that I'm stunned no one did before them, the part where they explain what Scientology is. What makes it even funnier is while all this talk about aliens and volcano's is going on at the bottom of the screen the words "This is what Scientologists actually believe". It's something that's so simple and yet so hilarious.
This is where South Park shone, it took a risk and even though they lost Chef (Who left claiming they were bigots, when in reality he was just upset that they attacked his religion) they won everyone over with their biting satire of a religion that needed to be taken on.