A Father's Love Is Maybe All It Takes (http://jennytork.livejournal.com/610208.html)

Thank~you for the rec!!! It was a wonderful story!!!

Thank you so much!!!!

This one sorta fits. It’s short snapshots of Dean taking over from John as Sam main parent and it’s told from John’s POV.
Choices (http://www.fanfiction.net/s/8500924/1/Choices)

Another self-rec, but this one is a little outside your request. Dean does act as the parent, making caregiver decisions, and Sam knows that Dean is looking out for him, but Dean's still the big brother.

Brother Mine (http://etrixiswriting.livejournal.com/52273.html)

Summary: John was out on a hunt when the call came: Kate Milligan was dead, and John was named in her will as the guardian of her son—his son—Adam. Pissed but knowing his duty, Dean pulled Sam out school during exam week, and they went to Windom in the thick of the Minnesota winter. 7-yr-old Adam was a lot like Sammy at that age, but Dean wasn't ready to accept him as another Winchester. Then the boy's life was threatened and all bets were off.

Did you read the other stories from "thoughtyouknewr"? They are all very good and in a lot of them, Sam loves Dean like a father.

Check out the story "no doubt" on fanfiction.net by silencesuffers. Great story and should be what you are looking for.

http://www.fanfiction.net/s/8525103/21/No-Doubt

Self-Recs

1) You are my father (http://likiel.livejournal.com/6047.html) by likiel

Summary: Dean saw Sam’s teacher asking him to stay a little longer and scowled but otherwise he didn’t move to his place near the door’s hall. He figured that whatever the woman had to say to Sam it wouldn’t take quite long. You don’t go debate with seven years old.

2) The (only) fanvid about Dean being Sam's brother ^^

http://www.youtube.com/watch?v=NgXqnxdRHA4&feature=share&list=UUIbaxauOyomJ7amVWHvYHGQ

3) My own SPN storyfinders request (http://spnstoryfinders.livejournal.com/7074944.html) on Father!Dean with a lot of recs given.

Enjoy

I don't think this is what you asking for but Sam used to call Dean his father when they were kids.

Facing the Music (https://www.fanfiction.net/s/7700197/1/Facing-the-Music) by Mr. Phich
Summary: Sam might finally be ready to listen, to hear and to understand. But even if he's not, it's time to face the music. Abused!Dean.

It's really nice and heart-aching but also contains sexual-abused!dean so read it for your own risk anyway :))