I wrote something thing called Burning the Midnight Oil (http://archiveofourown.org/works/2581289). (Cas / Dean / Benny.) It may not be what you're looking for because it's only 4800 words and it's fairly light due to my inexperience with the genre but I tried to give Dean some insecurities and have Cas and Benny help him with them. I do intend to explore the universe further, but I need to do more research / find my muse again. (It has a sequel that is more or less just kinda fluff.)

It was recently recc'd here but I enjoyed "Carry On" TamrynEradani. She took down her work because she's preparing to go legit but there are still PDFs available: here (http://www.mediafire.com/view/z9qlabcf3m8rd0b/Carry_On.pdf). (Bonus art :3 (http://destielfanworks.tumblr.com/tagged/carry%20on)) (Here is a masterpost of all her work. (http://shiphitsthefan.tumblr.com/post/126967477764/tamryneradani-fanfiction-masterpost))

Submersion
http://archiveofourown.org/works/3208745/chapters/6979427
Dean Winchester is the king of self destruction, living a messed up life sewn together by a single thread. To fuel his drug addiction and pay the rent, he has started working as a 'pay-by-the-hour' submissive escort. It's the perfect continued punishment for a sin that he was forced to commit.
He's submersed in a lake of depression, pain, and despair... destined to drown beneath the weight.

To make a nest
http://archiveofourown.org/works/1618769/chapters/3450002
For a kinkmeme prompt: Angels mate for life. But angel mates are not necessarily a single pair. Alphas bond with each other, but they don't become a family unit until an omega is part of the nest. Once that happens, the family unit is locked in for eternity.
Sam has met the alphas he wants to spend eternity with. Michael, Lucifer, Castiel and Gabriel are already pretty set, but they always knew they were missing someone.
Every one was surprised to discover Dean was an omega...


What you need
http://archiveofourown.org/works/216238/chapters/325118
There were surprisingly few search results for 'how to force your pain in the ass, closet masochist big brother to admit he wants to sub for you'. Go figure.

Dynamic equilibrium
http://archiveofourown.org/works/1178793/chapters/2403438
Estranged from his family, Sub Dean Winchester has been passing as a Dom for most of the past eight years, managing his biological need for Subspace with the occasional, unsatisfying one night stand and the banned drug Zero. After a hunt gone wrong, he’s taken into custody by the Department of Dynamics—much to his fury and disgust—where he meets DoD officer Gabriel Archangel. Gabriel’s family has run the DoD since before it was a government department, but Gabriel is the black sheep of the family, never quite living up to his protocol-driven family’s idea of what a true Dom should be like. Can two oddball mavericks make a go of it or will Dean’s need for freedom and Gabriel’s powerful, conservative family doom their fledgling relationship before it really starts?

The retraining of Dean Winchester
http://archiveofourown.org/works/1108581/chapters/2231285
Dean's been passing as a beta for years, until a bar fight and his own father leaves him high and dry without his pills in jail. Since omegas have no autonomy he has to be placed in a home and trained up in the proper behavior of a polite omega. Thankfully he lands a great case worker that manages to get him into a traditional Japanese style school. Dean isn't pleased with this but since the only other option is a state run mental hospital he decides to go along with it.



Edited 2015-09-22 04:45 am (UTC)

For your second request, Roots and Wings (http://archiveofourown.org/works/1093627/chapters/2201438) by elensule might be the kind of thing you're looking for. It's still a WIP, and there isn't much actual sex yet, but there's a lot of caretaking-via-scenes in it.

(Really, really not one for the John Winchester fans, however.)

Don't really know how to describe this except as smoking hot and amazing. She only has one Sam/Dean but here's hoping she does more!
http://archiveofourown.org/users/shaenie/pseuds/shaenie

I don't recall these stories specifically using the terms dom/sub, or alpha/omega, but I think they have the ideas you're looking for:

Time Wastes Itself (http://archiveofourown.org/works/56838?view_adult=true) by autoschediastic
Summary: Dean is about as shocked to be slammed back against the rough brick wall as Sam is over putting him there.

Playing Safe (http://archiveofourown.org/works/178265?view_adult=true) by callisto
Summary: Sam knows just what Dean needs after a tense hunt.

The Phthonus 'Verse (http://archiveofourown.org/series/6437) by leonidaslion
Summary: There's only so much jealousy a guy can take, and Sam's reached his limit ...