Nature is an Evil Bitch, or How Jared Learned to Stop Worrying and Let His Freak Flag Fly (http://archiveofourown.org/works/876091) - Jared knew he was a freak. In fact, he had a whole list of reasons that proved his freakiness. Oddly enough, the fact that he was a werewolf didn't even make the list because Jared had far more to worry about than the fact that sometimes he was furry and had four feet and a tail.
Not All Who Wander Are Lost (http://archiveofourown.org/works/2495495) (and its sequel, Woven Together (http://archiveofourown.org/works/2611802)) - The agonized keen that sliced through the chaotic bedlam of the raid had the fine hairs at Jensen’s nape standing to attention. Even as he straightened, eyes scanning to discover its source; he heard his men calling him. "Captain! You need to see this!"
The Perfect Mate (http://archiveofourown.org/works/823126) - Jared knew he was in trouble, knew he should have headed back to his pack weeks ago, before the first signs that his heat was coming had hit. But Jared had ignored his gut instinct to flee home, to return to his family, to be basically auctioned off to the highest bidder. He was an omega, the first of his generation, the first one his pack had had in many years. His whole life he had known that the alphas of his pack would one day fight over who got to claim him, knot him, fill him with their young.
Christmas Tree (http://archiveofourown.org/works/413275) (and its sequels, Coming Home (http://archiveofourown.org/works/413308) and Shattering Silence (Or, How Chad Knows Best) (http://archiveofourown.org/works/579470)) - A strange lone werewolf finds its way to the home of the Wolf-Pass Pack but how can Alpha!Jensen save a starving and dangerous Were who wants nothing to do with his own kind? Jared finds salvation by the light of a Christmas Tree.
(I have other good omega Jared links, but they're not weres.) (I just noticed you requested long fics. Realized a number of these are probably what you were looking for, but I hope you find some that are, like the Christmas Tree verse and the Freak Flag one.)
Ho Ho Ho (pt 2)
Not All Who Wander Are Lost (http://archiveofourown.org/works/2495495) (and its sequel, Woven Together (http://archiveofourown.org/works/2611802)) - The agonized keen that sliced through the chaotic bedlam of the raid had the fine hairs at Jensen’s nape standing to attention. Even as he straightened, eyes scanning to discover its source; he heard his men calling him. "Captain! You need to see this!"
The Perfect Mate (http://archiveofourown.org/works/823126) - Jared knew he was in trouble, knew he should have headed back to his pack weeks ago, before the first signs that his heat was coming had hit. But Jared had ignored his gut instinct to flee home, to return to his family, to be basically auctioned off to the highest bidder. He was an omega, the first of his generation, the first one his pack had had in many years. His whole life he had known that the alphas of his pack would one day fight over who got to claim him, knot him, fill him with their young.
Christmas Tree (http://archiveofourown.org/works/413275) (and its sequels, Coming Home (http://archiveofourown.org/works/413308) and Shattering Silence (Or, How Chad Knows Best) (http://archiveofourown.org/works/579470)) - A strange lone werewolf finds its way to the home of the Wolf-Pass Pack but how can Alpha!Jensen save a starving and dangerous Were who wants nothing to do with his own kind? Jared finds salvation by the light of a Christmas Tree.
(I have other good omega Jared links, but they're not weres.)
(I just noticed you requested long fics. Realized a number of these are probably what you were looking for, but I hope you find some that are, like the Christmas Tree verse and the Freak Flag one.)