2)ratherastory is the author you need:
Heaven Without You (http://ratherastory.livejournal.com/35070.html) - Insanely cruel hunters kidnap and torture Sam for starting the apocalypse.
Ex Crucio (http://ratherastory.livejournal.com/27803.html) - Sam gets nailed to a cross by some insane cultists thinking that's the way to stop him from becoming Lucifer's vessel.

Then there's From The Darkness (http://www.fanfiction.net/s/4231764/1/From_the_Darkness) by K Hanna Korossy, in which Sam gets abducted and subjected to painful experiments by crazy scientists because he's psychic.

And finally Finding Sam (http://www.fanfiction.net/s/5309810/4/Finding_Sam) in which Sam gets kidnapped and beaten up because some gangster boss (?) is mad at Dean. (Fair warning: I barely remember this fic, so I can't really vouch for its quality, but it ended up in my delicious, so it's probably not unreadable :D)