I know of two good crossovers between Supernatural and Good Omens.
One is Not Quite The Devil You Know. Authoress is playing a bit fast and loose with the metaphysics by merging the world and the plotline, but near as I can tell that's par for the course with Season 6 to begin with (only just finished sixth season). She certainly keeps to the spirit of the both source materials that each have their own version of the Apocalypse as well as can be expected. And most importantly, the story is in-character and genuinely entertaining. Could be a bit better, could be a hell of a lot worse.
For what I consider to be more straightforward all around goodness
When Summoning Please Watch The Wording. Very, very entertaining. And a one-shot.
Both are pretty good merges considering the source material. And no yaoi!
Yeah, I know, not the rec thread, but it seemed appropriate given the line of conversation. I figure if I'm gonna say, "Hey, there's some good stuff here," I might as well cite my sources.
Besides, if this inspires anyone, the world can always use more quality Good Omens fanfiction. Crowley and Aziraphale are also prone to be paired up for yaoi, yes, but their odd friendship is still a memorable one. Their perspective on humanity is also surprisingly compatible with the Winchesters.