Which is the Best Evil Church of Evil in Outer Space?

In a discussion about SF tropes that are ready to be put to pasture (or sent to the glue factory) the worthy robertjwizard writes:

“Another trope is the “let’s take the church, and make them an all-powerful force of sinister evil”. I dislike it for its transparency and I have never seen it well done. I think it because the author has a bone to pick rather than a story to tell – see Phillip Pullman. Another one is the evil corporation and for the same reasons.”

Let me ask anyone willing...