I know the Bajor/religion episodes are unpopular with many fans since Trek historically celebrates humanist ideals (among other reasons). Well, I'm one of those weird Trek fans who actually loves the Bajor/religion episodes. Here's a likely unpopular moment in DS9 which happens to be one of my all-time favorites. It's an exchange from "Accession," an episode which I read the producers had to fight the studio to make. I'm really glad they did even if my taste is unpopular.
Odo: Forgive me, Major, I don't mean to be difficult, but your faith seems to have led you to something of a contradiction.
Major Kira: I don't see it as a contradiction.
Odo: I don't understand.
Major Kira: That's the thing about faith. If you don't have it you can't understand it, and if you do - no explanation is necessary.