Survivors by maystone is a haunting look at what might have been, had Mal and Zoe not been as strong or as resilient as they are.
Tourniquet
by Pearl-o is crazy space incest all for me, I tell you. All. For. Me! BWA HA HAHAHAHAHAHAHAHA.... Also, it works on a non-CSI level as well, for all of you who get squicked by that sort of thing. Excellent examination of Simon's character, and how his wacky sister fits into his life.
So Long
by Kate Elizabeth is a lovely Mal/Kaylee story set in a future where Mal and Kaylee are recovering from losing the people they loved, and find each other. I know that sounds corny, but it's sweet as hell without being cloying, and Kate shows a very light touch with characterisation, as well as beautiful attention to detail.
Eavesdown by Shanna is a nifty "Serenity" missing scene that shows just how Simon got from there to here.
The Things That Haunt Us series by Eleanor K. is Mal/Simon that I can believe in. Packed with delicious and tantalising UST that about melts your monitor, each story slips in between the episodes and builds a complex relationship between two people who need each other, and keep trying to deny themselves and that need. Also, it has plot. In case you haven't noticed, LJC likes plot. Plot makes everything better.
Lapses and Leaps by Piper is a fantastic coda to Out of Gas which shoes Mal that faith isn't always something that exists only to be lost or broken.
Dong Ma? by ThatGirlIsabel is a nifty little story which does a great job exploring Mal's fatherly/big brotherly relationship with Kaylee, and how the Captain is handling (or not handling, as the case may be) her and Simon growing closer. Poor Simon; you gotta feel for the guy, with Mal on one side, and Jayne on the other, ready to kick his ass if anyone hurts their meimei...
Threading by Sara is a beautifully spartan and elegant vignette about Simon and boundaries.
Given Name by Azar is a peachy keen crossover with Buffy. I figured, with both shows sharing joss, that this would be inevitable, and had been dreading that eventuality. Azar and this story however made me 12 kinds of happy. I wish they could all be this clever and subtle and spot on.