DS9 had a lot of religious references. The whole ‘Emissary of the Prophets’ storyline.
The other series were pretty devoid of religion though. Well I didn’t see much of Voyager, but I know Enterprise really didn’t talk about it much, except maybe some of the Vulcan philosophy.
You're right, I forgot about that. I never much got into DS9, basically giving up on it during the third season.