a couple I forgot

The life and times of Lois Lane
http://archiveofourown.org/works/1007988
It’s not easy being married to a superhero. In fact, as Jensen’s learning, it’s nearly impossible.

Charades
http://archiveofourown.org/works/697816
Jared is a super villain, Jensen's a superhero. They fall in love in their civilian identities, neither of them aware of the other's extracurricular activities. Jared is faced with a choice when his teammates manage to capture and unmask Jensen: his friends and the life he knows or the man he loves."

and I found these couple but haven't read yet

The Gifted
http://archiveofourown.org/works/1173909
Jensen is one of the ‘gifted.’ Most of the world doesn’t know that his kind exists because the government hunts them down and takes them to a training facility. He’s treated well, but even a gilded cage is still a cage. Just ask the feral murderer that lives at the edge of the compound.

Pun, or, the Confession of an Unrealistically Reliable Narrator
http://archiveofourown.org/works/2467082/chapters/5470535
Dating your co-worker is hazardous at best, especially when you both work for the same superhero team. Dealing with an unexpected pregnancy with said co-worker—who’s grumpy and hormonal and knows how to turn into a direwolf at whim—is even riskier business. Finding out that your unborn baby has been prophesized to defeat the world’s greatest evil is just too much.
Now evil is out to hunt Jared, and everything he loves and everything he didn’t know he wanted but now can’t imagine life without. And really, he’s all for dying for his true love, his child, and maybe the world, but at least someone could have warned him before fate offered him up to be the modern day James fucking Potter.