if i remember correctly, The Simpsons did make fun of a religious sect once in "The Joy of Sect". it wasn't really about scientology but the cult leader pretended he was building a space ship and then he ran off with it with all the money he made from the followers but the space ship (which was only a bicycle i think) broke down and he got caught.

and the trivia bit on www.tv.com says that "It's very ironic that Bart would make that "Church, cult, cult, church" comment, since he's voiced by a member of the Church of Scientology (Nancy Cartwright)."

that episode has some really good quotes:

"Rev. Lovejoy: This new so-called religion is nothing but a pack of weird rituals and chants designed to take away the money of fools. Now lets say the Lord's prayer 40 times, but first lets pass the collection plate."

"Lisa: It's great that we can all think for ourselves again.
Announcer on TV: You are watching FOX.
Family (robotically): We are watching FOX"