Life, Death and Serenity by Shanna is a heartbreaking look at how the crew could and would survive losing one of their own. Stunning characterisation, excellent voices throughout—be prepared to get the sniffles.
Can't Look by Nicole Clevenger is set after "War Stories", as the Tams deal with their individual actions on Niska's skyplex. Lovely and chilling River in particular.
The Call by maystone is a very plausible and real scenario leading to Mal/Jayne, as wounded and terrified, they run from Reavers.
Glass Walls by Ana is an interesting look at the possibilities were Jayne and Simon to be captured by the Feds some time in the future. Not quite so much Oz as one might think, but it's curious to see how each would survive their particular circumstances. I'm not 100% sure I agree with her Simon, but her Jayne is dead-on accurate.
The Rape of Kassandra by ReaverPoet is a fascinating and spellbinding look at how River handles (or doesn't handle, as the case may be) simultaneously experiencing the past, present, and future. Also, it has both lovely Simon/Kaylee and sultry River/Kaylee moments.
Coming Home by sf fan explores the idea of how Simon would handle returning to his former social standing, now that he's grown accustomed to life aboard Serenity.
Forgive and Forget by Trisana McGraw is a lovely "Ariel" coda which explores Jayne's conscience, what there is of it.
Dancing Lessons and its sequel, In The Before by kirby crow are hot, sexy, subtle Simon/Jayne stories chock full of character development as well as sexual tension.
Feather Stitch by Ana is a delicate and lovely Inara and Kaylee story.
Friction Leads to Fire by Mara Greengrass is a Moonlighting-style riff on Mal and Inara.
Inadequate Comforts by Nicole Clevenger is a post-"War Stories" look at both River and Mal, which explores Zoe's choice, and the ramifications thereof.
Seeing Eyes by Jennifer-Oksana is a deft little River/Jayne piece set after "Ariel."