The Hunter Games (http://archiveofourown.org/works/519567) by theproblematique
SPN characters in the Hunger Games universe. When the Winchester bad luck strikes twice in quick succession Sam and Dean are forced to compete in the most brutal reality show ever created. It's impossible to escape the battlefield, hiding can only be temporary, and alliances inside those bloodstained woods last about as long as it takes for the other Hunter to figure out how to use your weapons. And then kill you with them.

Cardinal Hunter (http://zuben-fic.livejournal.com/81385.html) by zubeneschamali
Pacific Rim and Spn fusion. Saving people. Hunting kaiju. The family business. AU fusion with Pacific Rim, starting when Sam is at Stanford.

17 A.W. (http://archiveofourown.org/works/464829) by cleflink
Ever since the Deamhanan destroyed the Earth, Sam has spent his life in space. When a stranger named Dean tells Sam that he's the key to finding a weapon capable of killing the Deamhanan, Sam gets swept up in a fight reluctantly and finds himself far more attracted to Dean than he wants to be. Crossover of Supernatural & Titan A.E.

For apocafics, a few well-known ones in the fandom that you've probably heard of already:

Treasure (http://download.archiveofourown.org/works/402918) by sonofabiscuit
The light of Munin (http://download.archiveofourown.org/works/180210) by leonidaslion
Last outpost of all that is (http://gekizetsu.net/sn/lastoutpost.htm) by Gekizetsu

And a few less-known ones:

The book of Winchester (http://teashopmuses.livejournal.com/57215.html) by Selecasharp
Something Gold (https://www.fanfiction.net/s/7912945) by H.T. Marie
Dust & Shadow (http://archiveofourown.org/works/840771) by portait_of_a_fool
What is Always and Everywhere (http://www82.zippyshare.com/v/HggEBtS9/file.html) by portait_of_a_fool

Three more stories that fit the SF category, but that I didn't like as much as the others:

SPN-X-MEN Crossover AU (http://www.sinful-desire.org/archive/viewstory.php?sid=2632) by NeutralDeviance
Sam and Dean are Demon hunters who were born superpowered mutants. When Sam is kidnapped, Dean must turn to the X-Men for help...

Busy Being Born (http://archiveofourown.org/works/479492) by LadyAmarra, an a/b/o sci fi story.
In 2210, most of the Galaxy is part of Colonial territory. Society has advanced far beyond its keenest dreams, but male Omegas are still treated as basically worthless. For the longest time, Dean Winchester thinks he is just that: a useless Omega whose only purpose in life is to keep his uncle Bobby’s junk-freighter working while his father tries to find the raiders responsible for Mary’s death. But anything changes after Dean, desperate and unhappy with his existence, tries to kill himself – suddenly he has to face a new world far away from his family, a new group of people,, but most of all, he has to come to grips with the fact that he has never truly been an Omega but a subdued Alpha all along.

I think Therefore I Am (http://archiveofourown.org/works/464518) by oschun
Dean is a privileged member of the dwindling original population of North America that has been decimated by viral outbreaks and low birth rates. Human clones have been created to bolster the work force. They are a segregated underclass relegated to the status of soulless drones by their Geneticore creators and by powerful religious groups like the Mothers Union, who consider themselves to be the blessed vessels of God's greatest creation: the soul.
This is a story about the complicated relationship between two boys who are forced to grow up into hardened soldiers by a society teetering on the brink of civil war./