Most of these fall under Smart!Dean, and some are crossovers, which I'm not sure if you'd be interested in. But I figure I'll let you decide. Hope you find some fics you like!

Learning How To Fly 'verse
http://faithburke.livejournal.com/tag/supernatural%2Fstargate%3Aatlantis
Dean on Atlantis. Needless to say, the city loves him.
The author also has a lot of smaller fics and timestamps in the 'verse, so I hope you enjoy!

Loopy-Loop
http://faithburke.livejournal.com/53840.html
This is another Smart!Dean. It's usually recced, but I didn't see it here. High school Dean, outsider POV.

Unmaking
http://faithburke.livejournal.com/15009.html
"You have to stop it", Cas said. So Dean did.

Way To Kill
http://www.fanfiction.net/s/4281158/1/
Dean hunting on his own, while Sam is at Stanford. Crossover with NCIS. Dean appreciation and Smart!Dean.

Light and Dark
http://www.fanfiction.net/s/3439113/1/
Dean has a face-off with Michael. There are consequences.

Wolverines, Wendigos and Winchesters
http://www.fanfiction.net/s/5155714/1/
Crossover with X-Men. Dean and Logan (Wolverine). 'Nuff said. It's a WIP.

CherylW has some Dark Angel/SPN crossovers that I quite like because Dean is appreciated for being himself.
http://www.fanfiction.net/u/127403/
It's In The Genes, It Runs In The Family and New Family Traditions

Oops! Almost forgot one more by AlchemyAlice:
http://archiveofourown.org/works/245211/chapters/378117
On The Wings of War
I love this one. Awesome Dean, Destial (not really overt, but there).
The four Horsemen are not just people with fancy rings. They aren’t even demons with fancy rings. They are another species entirely, a force unto themselves, and Lucifer is kidding himself if he thinks that they are at his beck and call. They are separate. They are neutral. Dean Winchester is not built like them