Here are a few of my favorite season 6 fics:

The Road to Come (http://latentfunction.livejournal.com/418116.html) by latentfunction

Working together again is easy enough. Living together is the hard part. (Spoilers through early s6; goes AU after 6.03.)

I'd Burn This City Down (To Show You the Light) (http://lotrabc.livejournal.com/54636.html) by lotrabc

With Dean robbed of his memories and Sam of his soul, Sam's idea of looking out for his brother drives them in unforeseen directions, forcing both to weigh the age-old question of what makes us who we are.

Revisionist History (http://nutkin.livejournal.com/75866.html) by nutkin

Robo!Sam and Dean talk about the past. (This takes place at some point after 6.08, so there are general spoilers for all aired episodes! Being S6 fic, it's kind of dark, but it's also just kind of an ode to how much Dean loves Sam.)

All Fired Up, This Soul (http://community.livejournal.com/infatuated_ink/50563.html) by cherie_morte

Slowly but surely, Sam gets his soul back. That’s the easy part. (AU after 6.10 - "Caged Heat.")

Lead Us On (http://philalethia.livejournal.com/249970.html) by philalethia

The aftermath of Sam getting his soul back isn't at all like Dean thought it would be.

Since Feeling is First (http://queenklu.livejournal.com/233775.html) by queenklu

That he wants to think this is Dean yanking a leash should make his blood run cold, not aching hot. It should make him sick, angry, it should get his fucking hackles up and make him fight. (This was the prompt: Sam and Dean setting up a house, Dean taking a weird amount of pleasure in helping Sam fix up the house. Would love if a relationship developed because of it.)

He Breathes (http://rainylemons.livejournal.com/29098.html) by rainylemons

Set after Sam has be re-souled. Tender, angsty PWP. Dean's in the hospital, and even though Sam had tried to go back to the motel he was forced to come in again due to the blizzard outside. He stays the night in Dean's room and Dean convinces Sam that he's not too sick for sex.

Doubles (http://de-nugis.livejournal.com/22554.html) by de_nugis

Re-souled Sam needs reassurance Robo!Sam never hurt Dean.

Beautiful Scars (http://mickeym.livejournal.com/1330948.html) by mickeym

Coda to 6.12 ("Like a Virgin"). Sam and Dean's first time together again after Sam's been re-souled. Much love.

A Sweet Deal (http://callistosh65.livejournal.com/206683.html) by callistosh65

Coda to 6.15 ("The French Mistake"). Dean needs reassurance about what happened that night between Sam and Gen.