There's this one, by rifle53:

Watchtower!verse (http://rifle53.livejournal.com/3284.html)

It's weechesters, and includes not only Dean and Sam, but Adam too. Very cute :)

There’s a new one being written on fanfiction.net where John and Mary foster the boys.
No Ordinary Boys (http://www.fanfiction.net/s/8405435/1/No_Ordinary_Boys)

And there is Have You Ever Seen The Rain (http://www.fanfiction.net/s/4609261/1/Have_You_Ever_Seen_The_Rain) which has John and Mary adopting Dean and Sam.

Well, some one's already recs mine- thanks for that ;) so here's some more!
http://www.fanfiction.net/s/4975188/1/Lightness_and_Darkness AU Mary and John adopt two boys named Sam and Dean, who have been severely abused and refuse to be separated. However these boys may turn out to be more trouble than they're worth. Limp!Hurt!Sam Protective!Hurt!Dean Non-graphic sexual/physical abuse

(only Dean's fostered in this one also seems to be and abandoned WIP but what's there is good) http://www.fanfiction.net/s/6361040/1/Family AU. Dean's family has always been a nightmare...more specifically, his nightmare. When the tides turn and he's forced into a new family and a new life, will he see that family is more than the bad thing that goes bump in the night?

And I was sure I had one more titled In Shadow on fanfic, which I was sure I had saved, but now it's disappeared....

here's the link for In Shadow on fanfiction.net which I think is the one rifle53 mentioned (seconding the rec for her Watchtower verse BTW), not quite what you're looking for, the boys are fostered but not to Mary and/or John

http://www.fanfiction.net/u/1930123/UnholyMuse

It's an excellent story, thus far, but hasn't been updated in a couple of years :(