People have said that it's very difficult, with so many stories having been posted in the Fanfic Forum, to know which ones are worth the time to read. This thread will hopefully provide a way for readers to recommend good stories that they have read here.
I'd like to start with three favourites of my own:
"Star Trek: Lazarus"
A very innovative story set in the far future, as the ideals of the Federation rise from its ashes. It's accompanied by art that is every bit as fine as the writing.
"Orders of Magnitude"
by John Z. Drake
The first few chapters of a TNG novel that was submitted to Pocket Books (and rejected for reasons unconnected to its quality). This is a real professional effort, and it shows.
"Once more with starships"
The Buffy musical meets TWOK. Amazingly good, and very amusing!
Please, please, add your own recommendations, and help people find the treasures hidden in this forum!