Here are 3:

Denial (http://delicious.com/redirect?url=http%3A//jared4ever.livejournal.com/629.html)
Summary: Hunters catch up to Sam, and want answers about his role in the Apocalypse.

Potter's Clay (http://delicious.com/redirect?url=http%3A//reading1066.livejournal.com/61644.html%23cutid1)
Summary: Sam had an accident when he was a child. He has special needs. John is dead and Dean and Bobby still hunt; everything is like it is now but with Sam having special needs. Dean finds out about Adam, Sam is kidnapped by Lucifer, both brothers help him though the aftermath.

The Other Brother (http://delicious.com/redirect?url=http%3A//radiumgirl.livejournal.com/57817.html%3Fview%3D385241%23t385241)
Summary: Sam and Adam are pulled from the cage at the same time. Sam is not right, and Adam, stuck as his caretaker, is not pleased (the reason for Adam not being the same kind of drooling mess is up to the author). Basically, Adam really really doesn't want to care and holds onto his resentment for dear life, but Sam is all psychotic and hopeless so it's kind of hard. Cue grudging compassion and Adam dragging Sam around the country, hitchhiking with truckers and stuff while trying to keep Sam's lunacy on the down-low, in search of anyone else who wants to take him, anyone at all. When he finally gets his chance to be rid of Sam for good and for keeps, he barely has one foot out the door before he notices Dean/Bobby/the psychiatric nurse/whoever trying to calm Sam down and doing it all wrong. Breaking up is so hard to do.

It is! That makes this a double recommendation \0/

If you're open to a Criminal Minds crossover, this:
http://ohmynostalgia.livejournal.com/528.html
Was just posted recently; the characterizations of everyone, Adam included, are amazingly well-done.

Self rec? My Watchtower!Verse has Adam along with Sam and Dean being adopted by the Winchesters at an early age. It's an AU... http://rifle53.livejournal.com/3284.html

http://faithburke.livejournal.com/60739.html Dean Winchester gets a phone call that changes his whole life.

http://www.fanfiction.net/s/5237958/1/Growing_Up_Too_Soon What If Sam and Dean had Max's Childhood" Follows the boys life if John had too much tequila, and less demon hunting. Plus, Adam is included in the story! abusive!John, hurt!Sam,Dean,Adam

dollarformyname's Before Your Time Has Run Astray (http://dollarformyname.livejournal.com/27951.html) is one of my favorite Adam fics.

Absolutely anything by morkhan, she writes Adam really well and all her stories are fantastic. Be warned that most of them have somewhat soul-crushing angst, though. I especially recommend "Shiny Happy People" by her.

This Thing About Family (http://users.livejournal.com/_bluebells/36896.html)

Summary: Dean has two not-quite-complete brothers back from the cage and he's not sure that he's coping.

"Burn My Shadow" by neppie: http://neppie.livejournal.com/10506.html

Also, if you don't mind self-reccing I have a couple short stories about the cage that have Adam in them:

http://paper-rose16.livejournal.com/10744.html#cutid1
&
http://paper-rose16.livejournal.com/10273.html#cutid1

Hopefully you don't mind self recs :)
I have two Adam fics, cause I love him, they should also be getting an update soon :)

http://www.fanfiction.net/s/6714109/1/What_Could_Have_Been

http://www.fanfiction.net/s/5429938/1/Family_Of_Three