Here's a few of my favorites
http://dayspring.skeeter63.org/gold.html (http://dayspring.skeeter63.org/gold.html) by dayspring.skeeter63
AU. Dean's life goes in a whole other direction when Sam supposedly dies at age four. But while on the Shooting Team in the 2004 Olympics, Dean meets a tall, shaggy-haired swimmer. Can the yellow-eyed demon be far behind?

http://soserendipity.livejournal.com/4840.html (http://soserendipity.livejournal.com/4840.html) by soserendipity
“Dad’s on a hunting trip and he hasn’t been home in a few days.” Sound familiar? Sure, except this time, 18-year-old Dean confronts Bobby with the news. Because Sam? Sammy was taken when he was six – vanished off the face of the earth – and despite Dean’s best efforts, they've never been able to find him. John thinks Sam might be dead, but Dean can’t bring himself to give up hope that maybe, one day, he’ll have Sammy back at his side.

https://www.fanfiction.net/s/5092223/1/Chance-is-but-another-one-of-Fate-s-Playmates (https://www.fanfiction.net/s/5092223/1/Chance-is-but-another-one-of-Fate-s-Playmates) by Joby87
Weechester fic. One night, two men storm the Winchester household kidnapping the youngest and leaving the other for dead. Will John find Sammy in time or does fate have other plans for the child? Hurt Sam/Hurt Dean Scared/Fatherly John

I can't remember how long Sam had been kidnapped for in the last one, I think it was only for a few months but it's really good so you should look into that one too.

The Long Way Home https://www.fanfiction.net/s/3879595/1/The-Long-Way-Home AU. Dean makes a decision to force his Dad to become the father his brother needs, but when he finds out how badly his plan backfires, it's going to take everything he has with the help of his friends to bring Sammy home. !Crazy John!

The Boy Hunter https://www.fanfiction.net/s/10808672/1/The-Boy-Hunter AU. Sam disappeared 4 years ago following a row with his dad and Dean has been searching for him ever since following the trail of a infamous hunter known as the Boy hunter, this is the tale of his hunt and their reunion.