I'm pretty sure this is the one your looking for:
#1: Dean's Rules (https://www.fanfiction.net/s/7816101/1/Dean-s-Rules): Sam's been having trouble with bullies at school, but hasn't told anyone. Dean's been acting like he doesn't care, but is there more to the story? John's been a bastard like normal, but will he regret it when Sam's secret comes to the light?

and it has a Sequel if your interested:
Dean's Mistakes (https://www.fanfiction.net/s/7986341/1/Dean-s-Mistakes): Dean thinks everything is going great. Sam is healing, and that's all that really matters. All that changes when two men from the future randomly appear. Now they get to see what would've happened if he had never gone to that bar. Sequel to Dean's Rules (Not complete)

And then for #2:
- Never Have I Ever (https://www.fanfiction.net/s/10860478/1/Never-have-I-ever): When a harmless drinking game among friends takes a turn for the worse, the boys are faced with unresolved issues from the past. Hurt/Comfort
- Faith, Trust, and a Dog or Four (https://www.fanfiction.net/s/10999715/1/Faith-Trust-and-a-Dog-or-Four): Sam adopts a dog since, as Jody keeps telling him, he's allowed to have nice things. Somehow, thanks in part to the large dog impressing on Dean the need for an attitude adjustment, this leads to a bunker occupied by two humans, four dogs, an ex-angel, and an ex-demon. And when Charlie, Dorothy, and a surprise guest return from Oz just in time for Christmas, the fun really begins (Not really hurt Sam but he has issues where he doesn't believe he's good enough or deserves anything bc of Dean)
- Be Free (http://archiveofourown.org/works/4590144/chapters/10456350): AU from end of Southern Comfort. Sam takes Dean's words to heart, his mind throwing in its own two cents. Believing it is what will make Dean happy, Sam runs and becomes untraceable until it is almost too late. Dean calls in any help he can to find his brother, including angelic assistance. But finding someone with the knowledge Sam has, and who doesn't want to be found, the remaining members of Team Free Will better pull out all the stops, and fast. Sastiel. TRIGGER WARNING: self-harm, cutting, suicide. warnings in each chapter

Yes! This is the right story - thank you so much :)

Thank you for the other links as well, I will look into them once I'm home from work!

I have more if you want :)

#2
- Sam's Thirteen Reasons (http://archiveofourown.org/works/10655202/chapters/23579070): Three days ago, Dean came home to find Sam in the bathroom, wrists slit and barely breathing. Now, as Sam lays in the hospital unconscious, Dean finds a box of tapes left out for him to listen to. Curious, he presses play, but he never could have imagined what he would hear coming through the headphones.
- Five Times Dean Doesn't Kill Sam and One Time Sam Begs Him Too (Again): (http://archiveofourown.org/works/5781484/chapters/13324702) 5 + 1 set in season 5, directly from the point they're zapped onto the plane. There are some miscommunication after the voicemail, Sam thinks Dean wants to kill him.
- 8 Reasons Why (http://archiveofourown.org/works/7440937/chapters/16904332): Sam leaves Dean a set of cassette tapes and a marked-up road map after he commits suicide. Throughout the tapes, Sam explains how 8 people played major roles leading up to his death. Dean follows Sam's map and listens to his story, following in Sam's footsteps on a road trip from California to Kansas. Dean learns Sam's darkest secrets and sees a side of his little brother that he'd never known existed. Sam's tapes change the way Dean thinks about himself, his brother, and the world around him.
- The 'Problem' Verse (http://archiveofourown.org/series/135621): Really good series with multiple hurt Sam, overprotective Dean and Overprotective Cas

They sound very interesting, thank you so much for these links!

I always want more, I'm a fast reader ;)

get ready boy because I got a butload for 2#

1) https://www.fanfiction.net/s/5534978/1/You-could-be-happy
It's a wonderful life... or is it? Left alone over Thanksgiving break, Sam gets disturbing dreams of what his family would have been like, had he not been born. Featuring amnesia!Sam, sick!Dean, and remorseful!John (this one has Azazel in it!)
2) https://www.fanfiction.net/s/5316145/1/Heavy-Affliction
On a hunt, Dean and John learn some things about Sam he has been holding out on. Sad!Hurt!Sam15 Pissed!Angsty!Dean19,John
3) http://archiveofourown.org/series/18547
Sam doesn't go to Stanford. Everything goes downhill from there (personal favorite, really depressed Sam in this one)
4) https://www.fanfiction.net/s/4618333/1/Flick-of-the-Switch
When Sammy's visions go haywire and start attacking him physically, will the Winchesters and the other hunters be able to save him? Hurt/Limp/eventually Hypothermic Sam, Angsty, protective Dean and John
5) https://www.fanfiction.net/s/12188960/1/Leave-Normal-Alone
Pre-series. References to 7x03, The Girl Next Door. Dean finds a case of mass kidnappings, all children. John insists that it isn't supernatural and asks him to leave it alone, but 19-year-old Dean can't resist playing hero. If only he knew that meant drawing too much attention to himself and to Sam. Some cases are better left to the police. Dark themes and content
6) https://www.fanfiction.net/s/3556794/1/Soldier-Boy
AU. 18 yr old Sam Winchester doesn't go to Stanford like his Family thinks he did. Instead, he ends up at Parris Island and then the battle fronts of Iraq itself. This is the story of that Journey and after (not really hurt in this one but soooooo much angst)
7) https://www.fanfiction.net/s/7153701/1/Somewhere-in-the-Middle
Something is terribly wrong. Will Sam survive? Will Dean forgive himself? Will John be able to hold them all together? Seriously hurt/Sam; Seriously guilty/Dean; Seriously worried/John (amazingly told and in this one Dean is the one hurting Sam)

Do you want me to go on? And sorry I can't link even if my life depended on it.

Awesome! Thank you very much.

If you have some more (and have time to look the links up) feel free to add them :)
Can't ever get enough ;)

Ok you asked for it

1) https://www.fanfiction.net/s/5236194/1/Heat-of-the-Moment
When Sam is late home from school, John’s own brand of discipline goes a little too far. Sick Sam. Angsty/angry/guilty Dean. Angry/guilty John. Dean 19, Sam 15
2)https://www.fanfiction.net/s/3691343/1/House-of-Burden
Within its walls lives a family that has never been touched by hate, fire or the Supernatural… but for one (It is soooo much better than it sounds don't let it fool you)
3) https://www.fanfiction.net/s/10270160/1/Human-Born-Demon-Bred
Ten years ago, Sammy was kidnapped by demons, and Dean couldn't save him. The two are reunited when Dean summons a crossroads demon to save John's life, and Sam is the one who appears. Dean is convinced that Sam is still human somewhere deep inside. The problem is that nobody – not even his brother – agrees with him
4) http://rei-c.livejournal.com/845380.html
super secret agent Sammy rocks!
5)https://www.fanfiction.net/s/4259658/1/Your-Latest-Trick
Complete AU to BUABS. Meg threatened something much worse than Sam biting off his own tongue…
6) https://www.fanfiction.net/s/8166301/1/Third-Wheel
Sam Winchester didn't feel as though he was part of the family. It wasn't until a hunt that his brother and father realized that fact. John turns to Bobby Singer to help bring their family back together. AU angst/hurting/Sam, neglectful/John and Dean, awesome/Bobby, some language
7) https://www.fanfiction.net/s/3791492/1/Growing-pains
15 year old Sam faces another move, another battle with his dad, and the neglect that surfaces when Dean isn't around to be the buffer between them. Limp Sam to come, and whumpage for Papa Winchester and Dean too!
8) http://archiveofourown.org/works/4545330
Sam Winchester doesn't often feel hate.
Well, that's untrue.
His hate is just mostly reflected inward. (I don't know why but I really like reading about emotional hurt Sam)
9) http://archiveofourown.org/works/10947954?view_full_work=true
Sam Winchester shot himself in the head nine years ago, leaving Adam and Dean to pick up the pieces of their lives and take on their father's hunt for the yellow-eyed demon. Now they've been zapped back into the past, just in time to stop their teenage brother from pulling the trigger.

That are the best ones I have, just be carefull. I have almost none reading quirks or triggers, so just read the warning/ triggers. I don't want to be the reason why you have a bad day when you're supposed to have a good one because of hurt Sam

Thank you so much!

I don't mind sensitive themes, actually I kind of "like" them a lot for hurt sam - so don't worry :)