The modded BC I just don't "get". It seems extremely boring to me, nothing to do but set up battles, fly around and gawk at DS9. The add-on campaign has the worst voice acting I've ever heard, and the first mission was so hard I never got past it. But its worth tracking down a disc on ebay to play the campaign, *if* you can get one for 20-30 dollars with shipping.
By far, 25th and JR have the most "Trek" feel. AFU is similar, with better graphics, but the script isn't nearly as good as the previous two, which is complete with Spock-McCoy banter. Shat is audibly bored in reading his lines here and there, but otherwise it's good stuff. * If you get 25th or JR, make sure its the CD version - the floppy versions have no voice tracks!
BOTF is not worth what it sells for on ebay. It's basically a board game on a computer screen. Endlessly fun if that's your bag.
EF2 is fantastic. EF1 I haven't gotten to yet.
Hidden Evil is a lot better than reputation has it, and the reviews of being able to complete it in a few hours are BS. I like the unique graphics style - Hidden Evil is essentially an adventure game like 25th etc. A great bargain if you're a TNG and adventure game fan. It took me around 12 hours to complete it.
What I'm playing now is "DS9: The Fallen". Really nice game, and nice to be able to run it at max resolution on my circa 2005 PC. It's more of a FPS/Adventure game hybrid than EF2, sort of in the Tomb Raider vein. The levels seem a little visually monotonous/confusing in places, and its lacking Avery Brooks voicing Sisko. Otherwise very cool.