What you probably won't find in these fics: slash, porn without plot, romance, non-canon shipping. What you will find in these fics: great writing, great characterizations, great plots, great angst, and/or great humor. And darkness. Lots and lots of darkness.
"Ice in Crystal" by juliefortune
I'm a huge fan of Julie Fortune's Angel fics, so when she posted her first Firefly story I had to read it. It was my very first taste of Firefly fic, and boy what a standard does it set. Great plotting, perfectly realized characterizations, wonderful ensemble interactions, and Dark with a capital D.
"Scavenged" by salieri (troyswann)
It's possible that this is my favorite Firefly fic ever. Salieri's powers of description are incredibly vivid and yet perfectly spare. An unflinchingly dark story punctuated by perfect and heartbreaking interactions between Kaylee and Mal.
"Utopia" by salieri (troyswann)
Reavers. Jayne. Pretty much the scariest damn fic I've ever read. Read this one with all the lights on.
"Lex Talionis" by Tara LJC O'Shea
My favorite kind of fic--a plotty, action-packed ensemble piece interwoven with illuminating flashbacks. Great dialog, perfect characterizations, and lots of fantastic Kaylee-in-jeopardy angst.
"Reliance" by roseveare
This is the first in a series of connected stories, all of which are engaging and supremely satisfying. Perfect, plotty ensemble pieces with wonderful characterizations. Read them all.
"Rise Up No More" by agentotter
In my mind, this will always be Book's true backstory. Dark and heartbreaking.
"Divergence" by ana_grrl
AU snippets of what might have been for each of the characters had things been just a little bit different. I love these kind of "what if" stories--what if one simple choice had been made differently? How would that affect everything and everyone that came after? This is one of the best of its type I've read in the Fireflyverse.