My love is to like Ice, and I to Fire
http://users.livejournal.com/--tiana--/205208.html
In a world where superheroes exist, Jensen and Jared possess opposite abilities: Jensen controls ice, and Jared fire. Their first meeting results in Jensen's accidental near-death, so imagine his dismay a few years later when Jared joins his team. Team Alpha includes heroes with powers ranging from electrokinesis to teleportation. Jensen will have to face his painful past, his opposite-powered teammate, and his unexpected feelings for Jared, codename Phoenix, in that order. When a crew of villains sends the team into a tailspin, will this be a turning point for Jared and Jensen, or the end of all they've begun to build?

Super Hero verse
http://archiveofourown.org/series/53181
Jared is a superhero who doesn’t have the best grip on his powers or the best handle on dealing with the collateral damage that being a hero causes.

The last light I see
http://archiveofourown.org/works/5007877
When Jensen wakes up in the hospital, he wakes up confused and alone. There's no family or friends worrying over his bedside, no cards or flowers. The doctor quietly informs him of three things: his name, that he was beaten and mugged, and that he's tested positive for Super. On the long road of recovery from a brutal attack, Jensen slowly starts to piece together what kind of man he was, the kind he wants to be, and why the tall, ridiculously gorgeous gardener seems to hate his guts.

This Hell We've made (a favourite!)
http://archiveofourown.org/works/215020/chapters/323026
Except for the fact that they were both born with remarkable superhuman abilities, and a seething mutual dislike, Jared and Jensen have nothing in common. Turns out, though, that they may also be the only ones who can save each other from themselves.

Veterans of the Psychic Wars
http://psychicwar.livejournal.com/3181.html
When the invasion came, no-one was ready. Humanity faltered. We died by the thousands, then by the millions. Nations fell before them before the survivors could begin to hold them back.
The battles raged across the world, and communications became difficult, and then impossible. South America was gone. Before contact with Europe and Asia was lost, they were struggling, but surviving. In North America, the line held at last, a curve that stretched from Oregon to Louisiana. To the south, a battle-ravaged wasteland. To the north, the survivors and the refugees huddled beneath the shields of the Protected Zone, safe by the work of shield Psions who could form the only barrier that worked.
Along the front, soldiers waged war at terrible cost against an enemy that was truly inhuman. The tides of war turned on the work of battlefront Psions and their Guardians, elite warriors who could change the course of a battle with their skill and power.
At the most desperate moment in humanity's history, two men would face the battle. Jared Padalecki, a Psion whose power could only lead him to self-destruction alone in the face of the horrors of war, and Jensen Ackles, a Guardian fractured by his past.
Apart, they are broken and incomplete. Together, they just might save the world, and maybe even themselves.

Semiautomagic Au (a huge favourite!)
http://archiveofourown.org/series/4154
When Chris Kane, detective with the Special Investigations Unit, asks Jensen to consult on a gruesome murder case, Jensen doesn't know what he's getting himself into. Within days he has to find the killer, solve the case and try to stay alive, as apparently more than one powerful creature is interested in the outcome of this case. Or rather with the case never being solved

and this is hilarious - Jensen/Jared/Misha (think I'll have to go reread lol)
The life and times of a damsel in distress
http://big-banggang.livejournal.com/#big_banggang10235
Jensen Ackles has happily lived thirty-three years of his life as a reasonably successful, pretty much unknown journalist, until not one, but two superheroes suddenly have their eye on him. Now he’s known to every newspaper as the world’s most famous damsel in distress, and Jensen’s life has just gotten a lot more interesting and potentially dangerous. And sexy.
Hey, who knew he had such a mask kink?