Oh, this is my all time favorite category. :)

We Were Here (http://j2-wewerehere.livejournal.com/1579.html) - AU J2 This one is haunting and sad with lots of hurt for both boys, but the comfort is gorgeous when it comes. There's a sequel and a couple single scenes, too, if I remember correctly.

Flightless Bird (http://foolsdance.livejournal.com/9291.html) - AU J2 This is a slave!Jared fic with lots of oblivious but protective!Jensen. Nice happy ending.
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A Lesson a Day (Could Kill You) (http://www.sinful-desire.org/archive/viewstory.php?sid=2329&warning=5) - AU J2 "Jared has an abusive past, and when his boss sends him to learn how to become a flair bartender, that past is brought back in a storm of pain when he falls in love with his teacher, Jensen. But Jensen has his own problems and soon their attraction causes nothing but trouble, especially when Jared tries to face his fears."

Falling Forwards in a Backwards Land (http://queerly-it-is.livejournal.com/2889.html?view=387401#t387401) AU J2 - pornstar!Jared with a stalker. Hot and angsty and cute.

Hooker!fic (http://epicallytired.livejournal.com/239671.html) - AU J2 hurt!hooker!Jared and protective!Jensen

Fire in the Hole (http://insane-songbird.livejournal.com/183142.html) - J2 "At seventeen and growing up in a white supremacist camp, Jared's life is going nowhere fast. He doesn't feel like he belongs, but sees no way out - until the arrival of a new member shakes things up in the paramilitary group. Jared doesn't know whether he should be intrigued or afraid of Jensen Ackles, but when he gets caught in the power play around him coming to a head, he's left with little choice in the matter."

Who Watches Over Me? (http://archiveofourown.org/works/396200/chapters/651307) - J2 bodyguard!Jensen and moviestar!Jared with a stalker. This one is a little more Jensen-focused, but there's still lots of Jared and delicious man-on-man action.

The Ballad of the Invisible Boy (http://archiveofourown.org/works/1017905) and Two Headed Boy (http://archiveofourown.org/works/1997235/chapters/4327308) - S/D Oh my god, I just finished this one today (it's very, very long), and I think it might be my favorite Sam/Dean story yet. So much delicious angst, and such a gorgeous happy (finally) ending.

Cicatrix (http://askellington.livejournal.com/15633.html) - AU S/D This is a really creative world with convincing characters that are fresh yet remain true to their original essences. Love protective!Dean in this one.

Worth the Price (http://samdean.archive.nu/viewuser.php?uid=992) - S/D Another long fic with agonizing amounts of hurt for both boys (may be too much if you're looking for happiness, but the happy ending is there and worth the slow build).

Further and Further Out (http://samdean.archive.nu/viewuser.php?uid=992) and Rearrange Me 'Til I'm Sane (https://www.fanfiction.net/s/3956847/1/Rearrange-Me-til-I-m-Sane) - AU S/D (boys are still hunters) I just love the boys in these stories. So much hurt!helpless!Sam and protective!Dan with asshole!John (not abusive). Creative story and she writes so beautifully.

Full Moon, Fast Cars (https://www.fanfiction.net/s/3247697/1/Full-Moon-Fast-Cars) - AU S/D (boys are not related) These are great and so much fun. Love how neither boy is weak, but there are definite strong hurt!Sam/protective!Dean elements. This is the first story in a series.

Us and Them (http://archiveofourown.org/works/1765843/chapters/3777526) - AU Sabriel The hurt elements here are more emotional than physical, but this is the story that turned me onto protective!Gabe and Sabriel in general There's a WIP sequel that I'm avidly following. Sam is a tattoo artist and Gabe bakes pastries and c'mon, that's hot.

The Long Way Home (https://www.fanfiction.net/s/3879595/1/The-Long-Way-Home) - AU Gen Poor Sammy is hurt here in all the ways, but what I love the most about this story is the combination of protective!Dean with hurt! and badass!Sam. It's long with an equally long sequel.

Sure Got a Dirty Mouth (http://archiveofourown.org/works/411362/chapters/682610) - AU S/D This is really long WIP that I'm going to recommend anyway because it's just that good, maybe the best protective!Dean I've ever read. Since it's not finished, I can't guarantee a happy ending, but the happy moments throughout are strong enough that I have no doubt. :) Also, if you like Wincest, this one is HOT.

Give Thy Thoughts No Tongue (http://queerly-it-is.livejournal.com/2889.html?view=387401#t387401) - AU J2 Maybe not the best for your request since the hurt is minor and purely physical, but it's a great story anyway so I'm going to recommend it. :)

No Fortunate Son (http://www.sinful-desire.org/archive/viewstory.php?sid=2326&warning=5) - S/D Sad!Hurt!Abused!Sammy and Protective!Dean out the wazoo.

There's also one I can't remember where Dean is possessed and forced to rape Sam, with lots of long painful recovery for both boys. I'll see if I can find it.

Oh, the one I was thinking of is Passenger (http://supernaturalfic.livejournal.com/1615665.html) and With a Spit and a Prayer. (http://sn-fic.livejournal.com/540964.html) Very dark but good ending.

Thank you for your rec. There are some I haven´t read.