I have an amnesia (http://previous.delicious.com/chellexxx1/RPS+amnesia) tag, you might find something you fancy
xxx

These are all general-

Okay, so this was one of the first spn fan fictions I read and it was wonderful...
Ghosts in the Fog
Author: A-blackwinged-bird
COMPLETE. After an attack in the woods, Sam is left alone and with amnesia. Dean must find his brother and together, with the help of some friends, they battle the thing that prowls Black Hills Forest.
http://www.fanfiction.net/s/3035552/1/Ghosts-in-the-Fog

If you don't mind a self rec-
I Remember You
Author: gidgetgal9
Sam wakes up in a hospital with no memory. Will he learn the truth about what happened to him in time to save himself? S3 Not a death fiction! Beta work by Sendintheclowns and Floralia.
http://www.fanfiction.net/s/4557222/1/I-Remember-You

This is another fave of mine that deals with amnesia-
Broken Images by mizpah
Summary: Who was the handsome stranger brought to the mental institution in the dead of night - and what terrible tragedy from his past had reduced him to a broken, empty shell?
http://www.supernaturalville.net/viewstory.php?sid=1122

It has a sequel-
Fractured by mizpah
http://www.supernaturalville.net/viewstory.php?sid=1330

Hope this helps (All of them are J2)

The Winchester Identity (http://zuben-fic.livejournal.com/3108.html): Summary: A tall and handsome doctor is kidnapped by a mysterious green-eyed man who has no memory—but who definitely has a past. The J2 AU version of "The Bourne Identity". [Amnesia!Jensen]

Finding My Way Home Started With Finding You (http://ladyrhyanne.livejournal.com/13130.html): Scott McCoy is searching for who he is, literally. Seven months ago he woke up from a coma with no memory as to who he is or how he ended up in the hospital in the first place. Not entirely content at the ranch he has taken refuge at but not exactly ready to face an unknown past he`s convinced himself to stay until he has more money saved up. That is until the sleepwalking and the dreams start then he knows he has to start searching for the life he`s forgotten.

Jensen Ackles-Padalecki has never accepted (despite a murder confession from Chad Michael Murray) that his husband Jared is dead. He won’t believe it until he sees Jared’s body. Once the phone calls from Jared begin, he has renewed hope of finding him even if his friends refuse to believe that Jared is alive. [Amnesia!Jared]

It Feels Like Starting Over (http://sarlev-vanisa.livejournal.com/17632.html): Summary: A stunt gone bad leaves Jensen with no memory of the people around him, not even Jared. [Amnesia!Jensen]

Second Star to the Right (http://users.livejournal.com/__tiana__/222419.html): Peter Pan AU. Lost Boy Jensen, formerly Tootles, left Neverland ten years ago to finally grow up. Peter Pan had been killed by Hook, or so they all thought, and he saw no point in staying. Not long after a shocking visit from Tinker Bell, a stranger named Jared walks through the door of Neverland Candy and Coffee, and changes everything. [Amnesia!Jared]

Beholder (http://sandymg.livejournal.com/37314.html): Jared was passionate about the work he did with the animal shelter. Between that and living with Sandy, life was satisfactory. Until the cold night that the filthy, homeless man hidden in an oversized hoodie was dumped at the shelter and Jared couldn't just turn him out. Even if the man roared and called himself 'Beast.' Because under the hood, Jared was sure he caught a glimpse of a prince in those green eyes. [Amnesia!Jensen]

A Devil to Help Me Get Things Right (http://doodle-writes.livejournal.com/23394.html): It was in moments like this that Jensen knew that they would be together forever. Nothing would or could break them apart. Jensen was wrong. At 19 he was in love with Jared, full of plans and hopes for their future. He didn’t count on dropping out of college and driving Jared away with cheating and drinking being part of them. At 30 Jensen wakes up with retrograde amnesia, his last memories of being 19 and happy. As he struggles to regain his memory and find out who he is, Jensen has to face the harsh truths of who he became and how he treated Jared. Determined not to make the same mistakes again, Jensen starts to get his life back on track and try to win an engaged and angry Jared back. [Amnesia!Jensen]

The Measure of a Life (http://delanach.livejournal.com/39262.html): Jared was raised by his grandparents to have a love of the land they worked. Now he’s on his own, he’s struggling to hold on to the home he loves. When Jared meets Jensen, he’s not impressed with the spoilt diva, and the feeling is mutual. But after Jensen loses his memory, Jared makes a decision that throws them together. Based on the movie Overboard. [Amnesia!Jensen]

When Your Lover Breaks (http://sandymg.livejournal.com/28753.html):Jared Padalecki is filming the next-to-last episode of the fourth season of Supernatural. Jensen Ackles is his co-star, best friend, and as of this weekend, newfound lover. Jared’s life could not be better. Until a serious set accident shatters Jared's and Jensen's world. Jensen has lost himself and Jared is holding onto a memory. Can Jared love his partner enough to start from square one? [Amnesia!Jensen]

an oldy but a very very goody: http://memphis86.livejournal.com/8592.html 'A priori' one of the very first fics i read and memorized on LJ

I have 3 amnesia fics which I absolutely love but they're all Sam and Dean, and your tags said Jensen and Jared. Do you want?

I'd be interested in them, please. :)

The Plains of Lethe (http://meyerlemon.livejournal.com/879251.html) by meyerlemon. Gen.
Memories of me (http://samdean.archive.nu/series.php?seriesid=12) by gillianinoz. Wincest.
What remains (http://walkawayslowly.livejournal.com/1089291.html) by walkawayslowly. Wincest.

They're all written a long time ago, so you've probably read them?

Edited 2013-07-03 03:49 am (UTC)

Actually I haven't! Thanks so much! I look forward to checking them out. :)

http://kaylennz.livejournal.com/4828.html http://kaylennz.livejournal.com/4828.html

I see the moon is also Sam and Dean with Dean having amnesia. I just read this a few weeks ago and it was amazing.