For number one is it Oversight (https://www.fanfiction.net/s/4149156/1/Oversight) by kokoda2007 (https://www.fanfiction.net/u/1303844/kokoda2007)?

That's exactly the one! Thank you very much! :D

Slipping Through the Cracks (https://www.fanfiction.net/s/4821653/1/Slipping-Through-the-Cracks) is another great story by kokoda2007: "With the burden of hunting consuming their lives, John and Dean let their responsibility, for what should be their first priority, slip through the cracks. Pre-series. Sick Sam." (gen)

Sufferance (http://utsusemia.livejournal.com/41462.html) by utsusemia is a fave: "Eighteen months, two weeks and four days. AU from 5.04-that phone call was the last time Sam and Dean talked, but Dean never saw the future." (gen)

Country of the Heart (http://ratherastory.livejournal.com/194986.html) by ratherastory is also excellent: "After being hospitalized for meningitis, fifteen-year-old Sam finds himself put in a foster home while John is investigated for suspected abuse. Against all of Sam's expectations, his foster family turns out to be a caring couple with the kind of home Sam only ever saw from the outside while he was growing up, making him feel even more conflicted about the kind of life his own family leads. To make matters worse, John leaves town to go on a routine hunt in spite of his upcoming custody hearing, prompting Sam to wonder if his own father and brother might be relieved to have him —and his constant demands for normalcy— out of the picture. When his father goes missing, followed by Dean when he goes after him, Sam quickly discovers that they need him just as much as he needs them, and sets out to bring his family back together again, for good." (gen)

Touch and Go (http://archiveofourown.org/works/1842337/chapters/3960817) by themegalosaurus: "Tag to 9.19 (Alex Annie Alexis Ann) in which Dean realises why, exactly, Sam is so angry about what happened with Gadreel." (gen, with the bonus of heavily tattooed Sam ;))

If you're ok with AUs, I really enjoyed Catching Hell (https://www.fanfiction.net/s/11395674/1/Catching-Hell) by a_deed_without_a_name: "Sam Winchester is, perhaps, the greatest asset to the hunting community. His research, advice, and insight has reached countless hunters and solved innumerable mysteries. His life is solitary, but useful. That changes, however, with the delivery of a captured Knight of Hell who calls himself Dean." (unrelated Sam/Dean; the author warns for limp!Sam, but I'm pretty sure what he means is that Sam walks with a literal limp, because this Sam is pretty badass :))

(apparently I read a lot of AUs - here's a few more)

Kintsugi (http://brightly-lit.livejournal.com/42343.html) and Broken (http://brightly-lit.livejournal.com/44589.html) by brightly_lit: "Dean needs a new protective sigil tattoo, and he visits the tattoo artist other hunters recommend--the only person in the area who's precise enough for the work. Getting two words in a row out of the guy is hard labor, but undeniably worth it in the end." (gen; check the warnings on this one)

I don't normally read or recommend WIPs, but I am loving morgan's Stray (http://archiveofourown.org/works/2955065/chapters/6532100) (thanks to everyone who convinced me to give it a go): "Dean’s always been the type to pick up strays, even though he knows he can’t keep them. Most strays you just patch up and feed before you send them on their way. One day he runs into a stray he might actually want to keep." (Sam/Dean; regularly updated)

Edited 2016-01-05 01:23 am (UTC)

There's a lot of both Sam-whump and Sam-badassery in jassy's Regrets Trilogy (http://samdean.archive.nu/series.php?seriesid=95), which is sort of AU-y but still in the familiar Supernatural universe: "Sam refuses to allow the Crossroads Demon to have his brother." (Sam/Dean, Sam/others; again with the warnings)

I also really enjoyed Samuel Winchester and the Death of Azazel the Deathless (http://archiveofourown.org/works/54403) by vaingirlfic, in which Dean's still a hunter and Sam's a streetkid with powers: "Dean Winchester has hunted ghosts and creepy crawlies since he was a kid. It's been a crazy life but his Dad's been with him-- more or less-- and he could have lived with that. Until an encounter with a strange old woman leads him to a monster worse than anything he's ever had to deal with before. A monster's that's wrapped up with a shaggy haired stranger he wants more than anyone he's ever seen since he figured out what sex was for. Assuming he doesn't fuck it up, Dean's whole life may be taking a turn for the awesome." (Sam/Dean)

I have a bunch of hurt!Sam hurt/comfort fics saved here (https://delicious.com/elwarre/hurt!sam,hurt%2Fcomfort), if you'd like to browse.

(sorry about all the updates while I struggled to find the problem in the code :))