Oh, and some Mystery Spot fics (I went crazy a few weeks ago scouring for as many as I could find, lol):

Looking for Peace of Mind (http://www.fanfiction.net/s/5533316/1/Looking_For_Peace_of_Mind)
Summary: Coda to "Mystery Spot." Sam had read Dean's journal over and over in the months his brother was gone. Now, something was bothering him. Something he'd read. Did it really exist? Or was it just another of the Trickster's fabrications?

You Slay Me (http://www.fanfiction.net/s/5303415/1/You_Slay_Me)
Summary: Mystery Spot missing scene: In a loop full of the unexpected, he'd still never expected it to happen like this.

Slow Poison (http://www.fanfiction.net/s/5189533/1/Slow_Poison)
Summary: Mystery Spot missing day: The taco wasn't funny at all.

Wednesday's Child (http://www.fanfiction.net/s/4271137/1/Wednesdays_Child)
Summary: Mystery Spot/Jus in Bello tag: Sam's different, and Dean doesn't understand why.

Just Want a Glimpse to Know You're There (http://www.fanfiction.net/s/4145447/1/Just_Want_a_Glimpse_To_Know_Youre_There)
Summary: Coda to 3x11, Mystery Spot: The trickster was left behind by two hundred miles and three days, but Sam still wasn't Sam. Told from Dean's POV.

The Silence and the Noise (http://www.fanfiction.net/s/4144488/1/The_Silence_and_the_Noise)
Summary: Tag to 'Mystery Spot.' Dean died, and Sam had to learn how to live alone. Then the Trickster snapped his fingers, and Dean came back...but Sam didn’t. Even with Dean by his side again, he’s still living alone.

Holding Home (http://www.fanfiction.net/s/4753546/1/Holding_Home)
Summary: It was a long time to live without a soul. Tag to Mystery Spot.

Nothing Matters But the Part with the Numbers (http://pyrebi.livejournal.com/22843.html)
Summary: It would be almost frighteningly easy to step away from a time loop and simply...forget about it for a bit. Not on purpose, of course, but you know how things come up. And while it may only be a little while for the demigod creator, that could be forever in the mind of the only human who doesn't reset.

Free to Be You and Me:
Nothing Man (http://www.fanfiction.net/s/5495046/1/Nothing_Man)
Summary: AU coda to 5.03. Dean goes to Oklahoma after hearing about Sam's encounter with the hunters. What he finds when he arrives horrifies him.

Destruction (http://www.fanfiction.net/s/5410031/1/Destruction)
Summary: Spoilers for 5.03 -- Sam tests how serious Lucifer is about his promise warning: suicide attempts

Forgiveness is an Attribute of the Strong (http://dontknowmyname.livejournal.com/54913.html#cutid1)
Summary: A tag to 5x03: Dean let Sam walk out this time but he realizes now just how wrong he was. He’s not ready to let Sam go. There’s too much that needs to be said, too much left to be fixed.

Never Again
Summary: Lucifer's vessel. The words echoed in Sam's head. He won't let him win. Sam calld Dean. Dean races to stop him. Set after 5x03.

The Song Remains the Same:
Of Angels and Airwaves (http://community.livejournal.com/creators_hands/46473.html)
Summary: Coda to 5.13- Sam doesn’t quite make it back in one piece and Dean is there to take care of him.

Benders (I'm just copying from my bookmarks. Some may be more about Dean than Sam. Though, dunno how that happened. I'm such a Samgirl. lol):
You Pick the Animal (http://www.fanfiction.net/s/2805156/1/)
Summary: Inspired by 'The Benders"...what if they had decided to hunt Sam instead of trying to kill him?

Brought Back (http://www.thestade.com/khksn23.html)
Summary: Sam Winchester ran.

Proximity (http://www.fanfiction.net/s/2815328/1/Proximity)
Summary: Tag for The Benders. Dean and Sam get deeper into the woods, and not by choice. Dean thought Sam was safe with him, but it was more of a hope than a fact.

(http://www.fanfiction.net/s/5416493/1/Never_Again)