Devil's Arcade (https://www.fanfiction.net/s/4718216/1/Devil-s-Arcade) by Zubeneschamali
S4. While still dealing with the aftermath of the wishing well, Sam and Dean are taken by a group of hunters who will stop at nothing to find out the truth about Sam's abilities and how Dean managed to come back from the dead.

Land of the Lost (https://www.fanfiction.net/s/9466096/1/Land-of-the-Lost) by K Hanna Korossy
S5. Hunters tend to see things others don't. It was just a matter of time before some of them pieced together who let Lucifer out.

There's also 5X03 and 5X04 episode-linked fics like Idiot's Paradise (https://www.fanfiction.net/s/5409251/1/Idiots_Paradise) by Phx that deal with Sam being hunted down by other hunters, if you're interested.

Edited 2015-07-17 06:15 pm (UTC)

Broken Soul (https://www.fanfiction.net/s/8182175/1/Broken-Soul) by alxm: "The brothers have been separated for six months, unbeknownst to Dean that in all those months, his little brother was being held captive by a group hunters and tortured severely every day. When he finds that out, he goes for his rescue. And when he finally finds him again, he doesn't like what the months of abuse has done to his baby brother." (gen; a whole slew of warnings including graphic torture and rape)

The World Devours Me (http://varkelton.livejournal.com/45647.html) by varkelton: "Dean thought he was doing the right thing when he let Sam walk away from hunting.....away from him. Sam thought the separation was nothing more than he deserved. They both thought Castiel had found a way to keep Lucifer from finding them. Neither one of them knew how wrong they really were." (Sam/Dean; the hunter bit is in the beginning but the whole story's full of hurt!Sam; heed the warnings on this one, seriously)

Vengeance (http://ncc1701a.livejournal.com/22312.html) by ncc1701a: "John, Dean and Sam get kidnapped from hunters who have a grudge against John. There was this hunt a few years back where John withheld some information and people got hurt. Now they have the Winchesters and they want to play a game because how do you hurt John Winchester? Yes, hurt his sons! The rules of the game: John has to pull a piece of paper from a bag, he has to read out loud what stands on it and then he has to decide who of his sons has to endure what is written on it. After one of the men carried out the instructions on either Dean or Sam, it all starts again. If John doesn't choose they threaten to shoot both Dean and Sam. Instructions on the papers: methods of torture (like whipping, branding, electrocution, bastinado) or humiliating acts (like stripping in front of the hunters, giving one of the men a blowjob). (I want both boys over eighteen and hurt but I would like if Dean bears the brunt of it, John choosing him more often, Dean pleading with John to pick him)." (gen; again, lots of warnings)

Pray for Us Sinners (http://kaasknot.livejournal.com/9376.html) by kaasknot: "Sam and Dean get kidnapped, and are then tortured by a variety of BDSM kinks." (Sam/Dean; possible triggers should be pretty obvious from the summary)

If you haven't read the Freak Camp Verse (http://archiveofourown.org/series/5884), I highly recommend it. It's an AU with unrelated Sam/Dean and TONS of hurt!Sam at the hands of hunters. Warnings are pretty spelled out in the tags.

Idiot's Paradise (https://www.fanfiction.net/s/5409251/1/Idiots_Paradise) by phx: "Dean IS happy. He is. Until Rufus calls... AU Tag for 5.03." (gen)

Thirty Minutes (http://vail-kagami.livejournal.com/136953.html) by vail_kagami: "There are still hunters out there who don't like Sam very much." (gen; complete lack of a happy ending)

Ambush by Rachelly on fanfiction.net. An oldie but a goodie and Sam is put through the ringer!

Summary: Dean and Sam run into serious trouble when hunters gang together and make Sam their prey, and Dean, his only hope. 224k word count

Don't Let Go (https://www.fanfiction.net/s/4924056/1/Don-t-Let-Go)
When the boys are captured by the first 'friend' Gordon sends after Sam, one with a vendetta of her own, things go horribly wrong. Did Dean come back from the djinn's near-perfect world, for Sam, just to lose him now? Much Limp!Sam and Protective!Dean.

The Sound of Silence (https://www.fanfiction.net/s/9819396/1/The-Sound-of-Silence)
After Sam freed Lucifer, Dean says he can't trust him anymore. Tension rises as the brothers find out about their role in the Apocalypse. Sam really wants to regain Dean's trust so when he gets hurt, he doesn't tell him in fear of breaking their already fragile bond. But the consequences might make him lose more than his brother's trust. S5, Limp!Hurt!Sam, LittleLimp!Angst!Dean

The Weapon (https://www.fanfiction.net/s/9403050/1/The-Weapon)
AU after Season 5, Episode 3 "Free To Be You And Me". Sam takes Dean's advice and leaves. He doesn't get far though, before Tim and Reggie make a reappearance and this time they are not going to take 'no' for an answer.

Dreams and Desperation (http://jasmineisland.livejournal.com/11107.html)
When Dean threw the amulet away, it destroyed both of them.
The orchestrated trip to Heaven did far more damage than either angels or demons anticipated. Further misunderstandings, hurt, and anger drives them apart. Sam is led down a path of revenge, fire, and a desperate plea to an unlikely source. Dean is hell bent on revenge, but he is forced to realize that they have been played by masters that have had centuries to perfect their games. Now all he can think of is how to find his little brother before it’s too late.

The Thin Ice (http://buffyaddict13.livejournal.com/149086.html)
An average hunt turns deadly when a mysterious hunter kidnaps Sam and Dean, determined to exorcise a demon from Sam in order to "save" him. Sam and Dean insist Sam's not possessed but Libby doesn't believe them, and with good reason. Libby has proof Sam Winchester's a killer and she's not going to let him go.

xxx

Dark Side of the Hunt (https://www.fanfiction.net/s/6781485/1/Dark_Side_of_the_Hunt)
Post-6.14. When news of Sam and Dean's return to the hunt gets around, some old "friends" come back to find out what's going on. With Sam missing, Dean and Bobby race to find him before the rogue hunters do something to crumble the wall in Sam's mind.

Revenge is a Dish Best Served Cold (https://www.fanfiction.net/s/4915109/1/Revenge_is_a_Dish_Best_Served_Cold)
Sam is kidnapped and tortured by a hunter for revenge against John. Will he survive until his family can find him? LimpSam/AngstyDean/AngstyJohn

Denial (http://jared4ever.livejournal.com/629.html)
Hunters catch up to Sam, and want answers about his role in the Apocalypse.

Martyr for the Cause (https://www.fanfiction.net/s/7188438/1/Martyr_for_the_Cause)
Until he met the Winchesters, he hadn't known what family could be like.

The Truth and Nothing But (https://www.fanfiction.net/s/7241793/1/The_Truth_and_Nothing_But)
After Sam is found gunshot and bleeding out on a motel room floor, he refuses to talk about it. His increasing depression, and brooding silences, force Dean and Bobby to take drastic steps towards uncovering the truth. Who shot Sam Winchester and why?

xxx

The Deepest Conviction (https://www.fanfiction.net/s/5415859/1/The_Deepest_Conviction)
It takes a long time for Sam to say ‘yes.’ Spoilers for 5.04.

Heaven Without You (http://ratherastory.livejournal.com/35070.html)
Sam gets taken by hunters, who have nothing pleasant in mind for him.

Secrets and Deceit (https://www.fanfiction.net/s/5041040/1/bSecrets_b_and_Deceit)
Dean get's drunk, Sam gets the consequences when Dean doesn't keep his trap shut, in a hunter's bar no less. Season four spoilery-ness, Brotherly conflict, language and...yay

Caught Between A Rock And A Hard Place (https://www.fanfiction.net/s/4481560/1/Caught_Between_A_Rock_And_A_Hard_Place)
After John refuses to take a hunt he has been asked to do, another hunter takes drastic measures to ensure his participation.

They All Eventually Break (https://www.fanfiction.net/s/5417512/1/They_All_Eventually_Break)
Cas shows Dean the true reason why Sam had said "yes" to Lucifer. Tag to 5.04.

Hope you find something you like amongst this lot :)
xxx

All the World Drops Dead (http://mentholpixie.livejournal.com/17005.html#cutid1) by mentholpixie

Gordon does more than just try and blow Sam to bits and pieces and he's a more formidable foe than even Dean realized. Much h/c with tied!up Dean trying desperately to save Sam. Warning: Non-con

It has a couple sequels, they should be linked at the bottom (my wifi is giving me hell these days, apologizes for not linking them directly)