All the World Drops Dead (http://mentholpixie.livejournal.com/17005.html#cutid1) by mentholpixie

Gordon does more than just try and blow Sam to bits and pieces and he's a more formidable foe than even Dean realized. Much h/c with tied!up Dean trying desperately to save Sam. Warning: Non-con

It has a couple sequels, they should be linked at the bottom (my wifi is giving me hell these days, apologizes for not linking them directly)