I'm reccing "Secure the Blessing" by rahmi. It's a great AU where Sam makes a wish to protect Dean. They're separated - Dean has a new life with John and Mary, but his lifelong goal is to find Sam again. http://archiveofourown.org/works/639267

OH! I know an amazing , beautifully angsty gen fic that fits this description-- possibly my favorite fic of all time. Sam is taken from the family at a young age, John and Dean searched for him for years until John died, and Dean is carrying on the search. There are no words for how beautiful it is, and if you like it, there's even a wonderful sequel. Kintsugi, by brightly_lit: http://archiveofourown.org/works/1273438

Hope you enjoy!

Oh oh oh, I know one! Genesis (http://archiveofourown.org/works/2696183/chapters/6033437) by That_Certain_Slant_Of_Light. Basically an AU where Michael is Sam's father (yup, nephilim) and he, er, kidnaps Sam. It's new, but has regular updates. Haven't gotten to the part where Sam and Dean meet again though.

Got a few for you -

https://www.fanfiction.net/s/4315614/1/Bait
When the unknown is common knowledge and hunters are relegated to merely survivors, humanity is dwindling. With humans traded as currency, John and Sam find themselves with a new tool for their arsenal–a bait named Dean. Abused!Dean Protective!Winchesters
(WIP but still being updated - I really like this one)

http://zeppelin-123.livejournal.com/597.html
Au. When Sam and Dean where little, John and Mary got divorced. They both went separate ways. John becomes abusive and Dean is the victim of that. Dean has given up on people until one day he meets a boy in school named Samuel Campbell.

https://archiveofourown.org/series/81574
(Abusive!John, death!Dean, John leaves Dean at a hospital and Dean gets adopted)

https://www.fanfiction.net/s/5057112/1/In-Shadow
Pre-Series AU. The boys are put in separate foster homes after John is sent to prison. Five years apart in very different lifestyles sees them eventually reunited. Will their bond survive after years of separation and abuse? Contains abuse & rape.
(very angsty and be warned - it's WIP and hasn't been updated in a few years... but still, VERY GOOD)

https://www.fanfiction.net/s/5801127/1/Left-Turn-of-Fate
When Dean meets Azazel in 1973, the timeline is altered forever in ways that no one could have foreseen. Sammy embraces the hunting life, Dean ends up on a milk carton and John gets a new set of priorities, and an unexpected partner on the hunt.
(another WIP that hasn't been updated in quite awhile)

Sorry - can't do proper links for some reason today! Hopefully you'll like on of them though.

Am I able to get links to a couple of the ones you've mentioned? I love the raised apart trope and don't think i've read A Man Among Dogs, Into Your Hideaway or Semper Familia,..

Hi, here is one more!

Deaf Hunter fanfiction.net/s/6821414/1
(sorry link-function don´t work)

If you like dystopian AU stuff, Ringwall by bellatemple on AO3 was very good.
http://archiveofourown.org/works/3457004

Hi there! Soo this is an old request but i figured it couldnt hurt to add a couple more suggestions. There's a couple by Greenhairband that sorta fit what you're asking for. They're both WIP's though.

1. http://archiveofourown.org/works/6767815/chapters/15469216

2.http://archiveofourown.org/works/6763360/chapters/15457771