* This is a really beautiful fic../ very long and just full of everything that's wonderful! If you haven't read it, this ones a must.
The Doors of Time (http://felisblanco.livejournal.com/856417.html) by felisblanco
Pairings: Jensen/Jared (eventually)
Warnings: AU. This part spans them from early age until Jensen is 18 and Jared is 13. Spoilers for the ending of the movie The Piano (1993)
Rating: This part PG-13. NC-17 in part 2
Word count: This part approx. 65.000 words
Summary:
It’s not like he doesn’t try to fit in and make friends, he really does. It just seems like nothing he does is good enough for them. If he smiles they blink. If he speaks they stare. And whenever they see him coming they get this panicked look in their eyes like they want to run away and they don’t even know why.
Jensen knows why. It’s the same thing that makes his dad worry and his mom cry. That makes Nana tell his parents he’s going to Hell, not even caring that he can hear her.
It’s what makes him ‘weird’.

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Another two I've read multiple times:

Entwined Branches (http://www.livejournal.com/misc/get_domain_session.bml?return=http%3A%2F%2Fstrive2bhappy.livejournal.com%2F22126.html&sign=c09f0a5f997e864dc5388f2a77c6e1fd&t=1415749464)
Pairing: Jared/Jensen
Fits: All Time favorites of mine, a/b/o dynamics.
In a world where the government keeps a close eye on alphas, betas and omegas -- to the point of making certain everyone with these traits is mated by the time they turn eighteen -- it's no wonder the condition has become rather rare. It is, however, essentially unheard of to be unmated at thirty-three, but Jensen Ackles is an alpha who's good at staying under the radar. That is, until he's not and he's matched -- by bureaucratic decree -- to 18-year-old omega, Jared Padalecki. This is the story of how the two of them find far more than they ever thought they could.

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Title: Worth Having (http://the-green-bird.livejournal.com/18321.html)
Pairing: Jared Padalecki/Jensen Ackles
Rating: NC-17
Word Count: ~51,000
Warnings: alpha/omega, parental emotional abuse, one scene with the threat of non-con, knotting, Jared is 17 for most of the fic, but I wouldn't consider it underage

SPN Kink Meme prompt:
Jared's family has never hidden that they hate him for being an omega. They think it makes him weak and his existence dishonors their family. When they discover that the king's son is looking for a mate they jump at the chance to rid themselves of Jared and increase their social standing. They believe that something good should come from the blight on their lives.
Jared is anything but weak. He is intelligent and strong, not to mention that he isn't small. His siblings have taken great pleasure in informing him what the rest of his life is going to be like. Jared can expect to be barefoot and pregnant, his only purposes in life to service his mate's sexual needs and to provide him with heirs. They even suggest he will never be allowed to leave his mate's bedroom. Jared refuses to allow this to happen and vows to himself that he won't go down without a fight.
He's completely unprepared when the king's alpha son Jensen treats him like something precious and is interested in actually getting to know Jared better. Jared is wary, convinced that this is some sort of trick and Jensen will turn on him any second and treat Jared exactly as Jared's siblings said he would.


AND!(: Here's my delicious tag for
Favorite fics (https://delicious.com/infinitefeels/%2B%20all%20time%20fav)
A/B/O Dynamics (https://delicious.com/infinitefeels/%2B%20all%20time%20fav) A/B/O Dynamics - (2 (https://delicious.com/infinitefeels/kink%3A%20a%2Fb%2Fo%20dynamics))