I just picked up a book at the library dealing with the religons of Star Trek. There was a lot of religous beliefs during all of the series. TOS had tons of religous references in it and dealt directly ("Who Mourns For Adonis" for example). The Bajorans were deeply religous and that was a theme in both TNG as well as the entirety of DS9. DS9 was hugely based around religon. Voyager had some religous type themes from time to time.