Okay, here goes. I've got a lot of bits and pieces and I hope they're enough.
It's pre-series. wincest. Underage, Sam is 15 and Dean 19 when the relationship begins.
John and Bobby torture and kill a demon sympathizer's son.
In revenge, the sympathizer - the victim's father - kidnaps and tortures Sam, exactly replicating what John did to his son. It turns out the son wasn't infected with demon blood.
John, Bobby, Dean and a group of hunters rescue Sam. Dean is so angry with John that he won't let John help him take care of Sam in the aftermath.
Bobby guesses/knows about Sam & Dean's relationship.
And - I'm not as certain about this part - a legendary old hunter (OMC) gifts the boys with a set of magic knives, which they use to create a bond between them.
FOUND!
http://archiveofourown.org/works/411362 Gleeful thanks to
cmsserenity Mods - some of my original tags turned out to be wrong; can I fix that?