I read mostly wincest, so I only have one gen rec below.... so you may or may not find what you're looking for. All of the recs are set in season 1 or 2, and the last 3 have the guys doing a lot of researching. I hope you find something to enjoy:

God or Whatever (http://girlguidejones.livejournal.com/79556.html) by girlguidejones
Absorbing coda to “Faith” (episode 1.12). Sam’s POV; he’s reeling from worrying about Dean. Dean’s shaky from nearly dying and knowing another man died in his place. (Sam/Dean)

Carry Me Over the Sky (http://archiveofourown.org/works/21277?view_adult=true) by killa
Summary: Follows 2x08, "Crossroad Blues." Dean's running on fumes, and Sam's the match. (Sam/Dean)

Unthinkable (http://glassshoe.livejournal.com/947.html) by glassshoe
Summary: After a week of riding shotgun inside his own body, Sam needs to know that he’s the one at the wheel. This story takes place following the episode Born Under a Bad Sign (2.14). Features protective Big Brother Dean. (Gen)

Catch Your Death (http://archiveofourown.org/works/213150) by road_rhythm
Summary: In which Sam gets miserably sick, has a crisis of faith, and has to solve the case, anyway."

Takes place just after "Houses of the Holy" (episode 2.13), and Sam is still struggling with his faith issues. At the beginning of the story he's catching the flu, and during the story he manages to develop food poisoning too. At the same time he and Dean are tracking an angry ghost murdering young women. There is some (Sam/Dean), but it isn't the primary focus.

L'Oiseau de feu (http://rei-c.livejournal.com/807970.html) by rei_c
Summary: The demon makes a deal with Sam and Dean: one mystical creature in exchange for their father. The ensuing quest might take some time, but Winchesters never give up, no matter how tough things get.

So Sam and Dean encounter the Baba Yaga, vila (siren-like creatures), an alkonost (a bird with a woman's face), ghosts, the fae, and a three-headed dragon. While all that's going on, Sam's headaches and the powers indicating a slide to the dark side are growing. And there's the occasional amnesia, and the two of them waking up naked in the same bed without remembering how they got there... Missouri's here too. This is a link to the master page. (Sam/Dean)

Mixing Light to Light (http://rei-c.livejournal.com/751659.html) by rei_c
Summary: When a goddess traps Sam and Dean in a game with rules they don’t understand and an ending they don’t see coming, what other choice do they have but to play?

Sam and Dean have a run in with the Morrigan, and unfortunately she takes an interest in them. {' “A warrior and a seer. Not only that, but a warrior who fights the supernatural and a seer who has visions of death. I think she’ll keep an eye on you two.” '} Over the course of the following year on each of the Celtic holidays a new brand appears on both of them. They need to find out what she wants of them. (Sam/Dean)