I'd really like a Good Omens crossover where GO!Crowley and SPN!Crowley aren't the same character-- not that that can't be really good! I love the Arrangements!verse, for example, but I'd really like one that has both, and contrasts the two very different characters. As the various images floating around tumblr put it, GO!Crowley is "an Angel who didn't so much Fall as Saunter Vaguely Downwards," while SPN!Crowley is a human who, when given the opportunity, happily swan-dived down and did a double-backflip just to show off, and I haven't really seen enough fanfic exploiting the contrast.
I like Dean/Castiel and Aziraphale/Crowley (and since the three pairings often seem to go hand-in-hand, I'm fine with or without Sam/Gabriel).
Bonus points if the fic takes place after season five; double bonus if it's during season eight.