Babylon 5 and Star Trek:Deep Space Nine. Both have different emphasis. From what I remember of Babylon 5, the first human captain was supposed to be an alien race's reborn religious icon equivalent to Jesus. Then there was the whole light side/dark side aliens and a war against the "Shadows" (aka dark side aliens). But that one I vaguely remember since I was a lot younger. Deep Space Nine was based around a space station set in front of a stable wormhole, which the Bajorans (the population living on the planet right next to the wormhole) considered the home of the "Prophets," aka their gods. Quite a few episodes deal with how the humans deal with the religious authorities of Bajor. I also remember one episode where a teacher was talking about the wormhole "aliens" and was sharply rebuked in front of the children by a visiting Priestess for doubting the sanctity of the Prophets. There was quite a fuss over what to teach the children, similar along the lines of Darwinism/Creationism of today. The story eventually unfolded that the Commander of the station was the "chosen one" of the Prophets and multiple episodes dealt with him dealing with that role. The series ended with him going and staying the wormhole to learn from the Prophets (yeah I loved that show). Hope that helped you out a little.