Rather than rec individual stories, I'm going to rec a few authors that are still active in the fandom and still producing work. Most of what I'm reading in this fandom tends to be older stuff and if you look a post or two down, I'm also looking for newer crossovers, which aren't so easy to find in this fandom with a few exceptions. (SGA, NCIS, and The Sentinel. I've written a Criminal Minds crossover as well as a Torchwood crossover, but they are a lot older than what you are looking for.) Anything from the authors below are worth your time and sure to please.
I am also going to rec one of mine that is an AU crossover since you mentioned that originally and that some people seemed to have enjoyed. The series was written in 2011 and starts off as pre slash and is very close to my heart. It's a bit older than what you asked for, but it continues with a second series related to this one and featuring Destiel. It's called The Barking Dog Winery and is SG1 and SGA and eventually SPN.
no subject
http://archiveofourown.org/users/Paian/pseuds/Paian
http://archiveofourown.org/users/jdjunkie/pseuds/jdjunkie
http://archiveofourown.org/users/Princess/pseuds/Princess%20of%20Geeks
I am also going to rec one of mine that is an AU crossover since you mentioned that originally and that some people seemed to have enjoyed. The series was written in 2011 and starts off as pre slash and is very close to my heart. It's a bit older than what you asked for, but it continues with a second series related to this one and featuring Destiel. It's called The Barking Dog Winery and is SG1 and SGA and eventually SPN.
I hope this is helpful and gets you started!