Uh don't wanna be a downer before I make my suggestions but in the very first thread Naraht's links don't seem to be working. They load which I assume is supposed to be a TrekBBS FanFic thread but there is a message saying it can't be found or some such. Just thought I'd point that out becuase I'd really like to check out a couple of the suggestions listed there.
Oh and I nearly forgot...but if anyone can track down the link, or maybe you can ask him to email it to you, but Ptrope's "Endeavour"(his version of Enterprise) is an excellent read and IMHO the way the show should've been written. It's not finsihed yet but well worth the read.
Anyways I would like to second the suggestions of Emperor Tiberius, Naraht, Gjob there work is some of the finest. Along with a former member named Krag(I think that was his name, he wrote a bunch of excellent mirror universe type stories and did a awesome Dominion/Borg War story as well a couple years ago. There was a poster here that had a story called "Epilogue" that was like an extra hour of "Endgame" it basicly just wrapped up what we didn't seem to get on screen. If anyone can remember the thread...please post it.