The rest are a bit more AU, not like non-hunter AU, but very very cannon divergent. They're really good and I recommend them whole-heartedly.

Won't Get Fooled Again (http://archiveofourown.org/works/2707712/chapters/6059834) by Safiyabat
When a creature claiming to be an angel comes upon Sam and Ruby in a motel room claiming he can help Sam train to rescue Dean from Hell, Sam agrees to work with the mysterious Castiel. It doesn't hurt that the handsome stranger tells him that his abilities don't damn him and makes him believe that he might be worthy of affection. When Dean is safely alive again, however, things change. Castiel's orders require him to sever ties, leaving Sam adrift as the road to the Apocalypse appears before them. What will Sam do when he begins to realize that angels are not what he believed?
---~50k, their relationship is very strong, features Unwilling Boy King Sam, but not Evil Sam, AU-Cannon Divergence to Season 4---

I Have Stood Here Once Before (http://stangerine88.livejournal.com/54392.html)
Centuries into the future, the world has ended. Neither Heaven or Hell have come out victorious as the last human soul is wiped from the war-savaged Earth. In a fit of desperate rebellion, Castiel goes back to the start, back to November 2nd, 2005 to prove once and for all that people make their own destinies. Only fate's a fickle bitch when you try to pull one over on her and Castiel finds himself in a time in which Sam Winchester is a far cry from the hardened hunter of his memory.
Already plagued by waking visions, Sam finds himself left with this mysterious angel as his only ally. Forming a delicate, somewhat awkward friendship, Sam and Castiel set out to find the Colt and to stop Azazel from freeing Lilith and starting the Apocalypse. Dodging Heaven, Hell and two over-protective Winchesters, the alliance formed through necessity slowly becomes something not even Sam could have seen coming.
---Time Travel Fic, Season 1 AU, 48k, It's one of my favorites---

Out Where The Shivers Won't Find You (http://archiveofourown.org/works/294134) by discreetmath
After Castiel rescues Sam from Hell, he sets him up in a cabin in the middle of nowhere to recuperate, and to give his soul time to heal from the damage it suffered in the cage. When Sam experiences violent, frightening flashbacks to his time with Lucifer, Cas offers a solution, but neither one of them anticipates the way their tentative friendship will change. AU after 5x22.
---15k, angst, healing, <3---

The Spaces Between Us (Has No Hold) (http://archiveofourown.org/works/1174396/chapters/2392592) by AllThoseOtherWorlds
What if things in the pit had gone differently? Michael and Lucifer don't torture or hurt Sam, but things take an unusual turn when his memories are unlocked, and he, Dean, and Castiel must deal with the consequences. Bobby just expects them to pitch in on the research while they're at his place.
---I love this one, has angel!sam, and a bit of memory loss, AU to Season 7, lots of Cas/Sam bonding/angsting/forgiving, 2 companion pieces---

Hope you found some you like!