"Again" by Lisa Countryman. This can be found at Unimatrix Seven. The story is J/7 and exactly what I like in fan fiction. A good story, well written characterization and witty to boot.
"Just Between Us" by Gina Dartt. Episode one of the wonderful JB series. I first read this episode in an archive and then spent the next three days wishing that there was more fan fiction like it. And then I stumbled on the The Captain's Quarters where, to my umitigated glee and joy, I found six more chapters. There are now 50 chapters and Janeway and Seven are back in the alpha quadrant. GD has started a follow up series called Millenium which is equally good.
I thought I ought to list at least one more of the JB series but in fact I have decided to list a sub series of three episodes 24-26, namely "JB Battles", "JB Fortune & Folly", "JB Lost and Found". Why these three? Well there are at least four other individual episodes which I re-read but I always read these three together. TPTB could learn something from Ms Dartt about how to write sustained story arcs within a coherent overall series. Again all found at The Captain's Quarters.
Did I mention I liked Buffy The Vampire Slayer? Well I particularly like those written by the Pink Rabbit Consortium. And one of my favourites is "It All Depends On Your Timing." Why do I like this one? Well it's funny and sweet and well written.
Returning to Voyager but T/7 this time. I really love "Raise A Bright Flag" by DiNovia. Originally posted as a one off, DiNovia is planning to incorporate the story in a series but it is perfect within itself. The story can be found at Stovokor Collective
No list of favourite f/f fan fiction should omit (this is a bold statement) the following: "Sustenance" by Tenderware. An original and extremely well executed J/7 piece. Located at the spectacularly named Delta Quadrant of Venus
Next up is another J/7 piece namely "Beginnings" by Lisa Countryman. Another good story - the only improvement? B'Elanna should have got the girl. Again to be found at Unimatrix Seven
I don't think any list of favourites should miss out on a good Mary Sue and my, not very original, choice is "Falling" by Wonko which lives at How Do I Love Thee.
"The Love She Knows" is a really good story from Vaxen. It is quite a mournful J/7 in some ways but was written in answer to an angst-filled story by Boadicea.
And finally J/7 from the Pink Rabbit Consortium who do every thing well. "Not Just Strip Poker."