Second Glances verse
http://archiveofourown.org/series/606505
Sometimes, a pretty face is hiding a very scary man. Just a day in the life of a mob boss and the love of his life.

The HellSpawn verse (it takes a little while till you get the whole picture)
http://archiveofourown.org/series/489715
Seven years ago talented pool hustler Jensen Ackles fled LA for his home state of Texas—with a price on his head and HellSpawn MC on his tail.
Now, Jensen’s past has finally caught up with him. His debt has been bought out by the Vice-President of HellSpawn, Jared Padalecki, who expects Jensen to satisfy his dark sexual appetites. But even worse than life as the VP’s beck-and-call boy is the very real possibility that Jensen just might be falling for the sinfully sexy biker.

Another Day at the Office verse
http://zuben-fic.livejournal.com/97974.html
Jared thought his boyfriend was a nerdy but cute accountant, not a super-secret agent who's the only one who can save Jared's life.

Black Jared and the proper Molly (there is a sequel too)
http://archiveofourown.org/works/2148468/chapters/4694823
The most ruthless and notorious pirate of the Caribbean, Black Jared, thought he was just getting a pretty bed warmer when he made a deal for gold and the young man's body on the deck of the British merchantman. The boy shyly succumbed to his advances one night only to turn and viciously murder a whore in a jealous rage, and ballgown, the next. Nothing could have prepared the pirate captain for the young tutor’s sly intelligence or mercurial nature. At first, he rolled with the boy’s changing moods, but, with his crew’s warnings ringing in his ears, a time of reckoning was soon at hand.

In my left hand
https://www.dropbox.com/s/l218p0gokptv8gw/In%20My%20Left%20Hand.pdf?dl=0
In which Jared is a crime lord and Jensen is his boyfriend.


these ones are maybe sort of what you are looking for, more the underestimated and stronger or different to what people think.....

Open Road
http://archiveofourown.org/works/4637088/chapters/10574286
Jensen is a young Harvard med student with a bright future ahead of him and Jared is the hot-headed member of the renowned biker gang 'Black Legion'. When their two worlds collide and their lives become intertwined, will they both survive with their hearts intact?

Yoko Ono's got Nothing on Jensen Ackles
http://archiveofourown.org/works/891957
Jared Padalecki has lived the hard-rock, hard-drinking lifestyle practically since the day he left his home and his alcoholic father. Jensen Ackles has been sheltered after disease almost cut his life far too short. Can they forge a path together or will forces larger and stronger force them apart.

The War Prize
http://archiveofourown.org/works/431786
Jared, Monarch of Valdesco, did not want to get married. He especially didn't want a political marriage to someone who was part of the negotiations for peace. There was no way he could deal with a spouse whose culture was completely alien to his own.
Jensen Ackles was appalled to be the War Prize his country offered up as reparations. He sincerely did not want to go from being the High Chief's youngest son to being without status. And mostly, Jensen did not want to live in a country that was so technologically advanced that he had no hope of beginning to understand it.
But, like a lot of things in life, neither one of them was going to get a choice about it.