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I've been using the Distant Stars mod , it has some good enhancements and is kept updated (great job guys)
Sacrifice of Angels 2 is a really good Star Trek mod, it's still a work in progress but is very playable (I can't wait to see the final product, kudos to these guys too).
The first mod I played was the Mad Scientist Mod. It adds a lot of technology enhancements (not really any new techs just more levels). The original creator is no longer keeping it current, but Harpo9999 has tools and instructions on how to update it.
I like all of the above mods and won't hesitate recommending any of them.