This is not a comprehensive list of fics with Adam Milligan as a main character, there's way too many to even try to list them all. So this is a collection of the ones I enjoyed.
** = I love it, * = I like it, ^ = self-rec
* A Friend Given By Nature by mollrach13
T, Complete, >14,000
- Stanford Era. Adam's mom is killed and the only contactable family number is Sam. First shocked, but accepting, Sam takes on the role as older brother and caretaker with pride and worms his way into Adam's heart. But going to school, to work, and making enough money to support two people is a lot harder than Sam had anticipated.
Before Your Time Has Run Astray by this-ism that-ism
T, Complete, >10,000
- It doesn't matter how far or deep he buries himself, his brother always sniffs him out. Post "Swan Song". Adam fic.
Brother Mine by etrix
T, Complete, >29,000
- 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.
Finding Calm in a Storm by TrishaCollins
No rating, Complete, >50,000
- A drunk driver and Kate cross paths, leading John to panic and get there as soon as he could for her and Adam.
Which leads to Kate meeting the boys, and the boys meeting Adam. Nothing goes exactly as John had planned, but maybe the results will be better for everyone.
Finding Purgatory by mollrach13
T, Complete, >2,000
- Purgatory is one of the back doors out of the Cage. Dean encounters a familiar face fighting his way back to the surface.
He Ain't Heavy by deanstheman
T, Complete, >10,000
- What if Sam wasn't the only Winchester freed from the cage? What if Adam wasn't given a wall to hold the horrors at bay? How would Sam and Dean deal with the mess that used to be their brother?
Hell's Angels by CeCe Away
T, Complete, >21,000
- Sam screamed, turning to fold Adam into his own body, offering what little protection he could as the thrust of pain speared his back.
** Hell Hath Such Fury by axilet
T, Series, >4,000, Warning: [torture]
- There's still a Winchester in Hell. Sam and Dean haven't forgotten.
^ Inosculation of Two Souls by Rirren
E, Complete, Sam/Adam, >19,000, Warning: [torture, noncon, mental illness, self-harm]
- Trapped together for centuries in the cage, Sam and Adam wrap around each other like inosculating branches of two different trees.
It Gets Better by grlkat
K+, Complete, Sam/Adam, >1,000
- The Cage spat him back up and his older brothers didn't really know what to do for him but Sam tried.
** Keep Your Secrets by loneredsock (alternative link)
No rating (M), Complete, Dean/Adam, <5,000, Canon AU
- Adam meets Dean in a bar. There is a one night stand, and the morning after is weird as fuck.
* The Man Who Wasn't There by minviendha
No rating (M), Complete, >3,000, Warning: [torture]
- Sam thinks he's going crazier. He isn't.
Out of Aberdeen by irnan
K+, Complete, >2,000
- You call this the afterlife? I call this a horror movie. What's more, I call this a horror movie I wouldn't pay to see!
O Sweet Brother of Mine by kels
T, Complete, <2,000, Dean/Adam, Warning: [underage]
- When Adam was 12, he met his father for the first time. The next night he met his brother, Dean.
* The Other Brother by kettle_o_fish
No rating (K), Complete, >3,000, Warning: [mental illness]
- 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.
* Passenger by scorpiod1
M, Complete, Sam/Adam, >5,000
- Sam’s brother is dead. Adam’s mom is dead. Together, they try to cope and survive, despite their massive issues. AU from No Rest For the Wicked.
Shell Game by rivkat
MA, Complete, Sam/Dean, >20,000, Canon AU
- Sam and Adam Winchester know when they’re being conned. Problem is, this new guy Dean Milligan seems to really be their half-brother. Adam is unamused, Sam is unfazed, and Dean is inappropriate.
We Are Still Gone by guardiancastiel
M, Complete, Sam/Adam, implied past Sam/Dean, >12,000
- Sam and Adam are inexplicably back from Hell but they do not have the problems you think they might have. Their problems are more steeped in their emotional troubles and without Dean they look for comfort in each other which only complicates their situation.