2. I have a list here (https://sites.google.com/site/fanficthematic/home/supernatural/accidental-incest#am)of Sam/Dean fics where they both lose their memories and realize they are attracted to each other.
I also have a list of fics (https://sites.google.com/site/fanficthematic/home/supernatural/accidental-incest#ui) where one of them doesn't know they're related and this leads to Wincest. The majority of the fics in this list include amnesia, it's fairly easy to work out which from the summary, so I'll leave you to browse through it at your leisure but I'll just give you my favourite fic from that list:

Blue Skies From Rain (http://lovesrain44.livejournal.com/26355.html) by lovesrain44 (AO3 (http://archiveofourown.org/series/11774))
MA, Complete, >170,000, Mostly Bottom!Dean, Warning: [mental health issues]
- The morning after Sam rescues Dean from the djinn, Sam and Dean go back to the warehouse to take care of the bodies of both the victims and of the djinn. But instead of what should be a simple clean-up job, Sam and Dean are sucked into a nightmare world brought about by the djinn’s last dying act of revenge. (Takes place directly after What Is and What Should Never Be.) What do you do when you wake up in a mental institution and you think your brother is dead?

Wow, that is a really long list! Thank you so much! Thanks to your list I just read through the Outlaw Dean Winchester, which was amazing. A love a good supernatural Old West AU. I can't wait to read through the rest of the fics. :)

http://memphis86.livejournal.com/8592.html

one of the first stories I read on LJ and still a great memory!

That looks really good, thank you! I'm adding to my reading list, I can't wait to read it. <3

Sam/Dean
What Remains (http://walkawayslowly.livejournal.com/1089291.html) is my favourite amnesia!fic. It's a little bit of your #1, a little #2, I guess.
Summary: In Jefferson, Texas a man ends a generations-old curse and saves all the town's children, but completely loses his memory in the process. When it's discovered that he's a wanted criminal, the town comes together to conceal him out of gratitude for what he's done for them, giving him an apartment, a job and a whole new life. It takes seven months for Sam to find Dean, and when he finally does, he has to adapt to being around a man who has no idea that he used to be Sam's brother.

I See The Moon (http://kaylennz.livejournal.com/4828.html) is more your #2.
Summary: Sam had known how Dean felt about him when he'd left for Stanford. His own feelings weren't so clear. He'd needed time away from it all, hunting, his father, and especially Dean. It took him five years and a degree he hadn't planned on to realize there was only one person he wanted to share his life with. He'd never considered the possibility that Dean would move on without him...or that something could happen that would erase him from his brother's life completely.

J2
Beholder (http://sandymg.livejournal.com/37314.html) is definitely #1.
Summary: 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.

You're The Dream Of A Lifetime (http://sammyndeansgrl1.livejournal.com/87022.html#cutid1) Not really any of the 3 categories, but a great amnesia!fic all the same.
Summary: Jared is married to an extremely abusive man. One night, his husband discovers Jared’s intention to leave him – and the unthinkable happens.

These look very good, just what I was hoping for. I have never read an RPF amnesia story before, I am excited to give that a try. Thank you so much for your help! <3

Have you read any of these?

Only Sweeter (http://archiveofourown.org/works/3188) by rivkat

We Came From the Breeze (http://lazy-daze.livejournal.com/486002.html) by lazy_daze

Give the Lie (http://archiveofourown.org/works/178577) by dreamlittleyo

Stranger That I Used to Know (http://infatuated-ink.livejournal.com/88523.html) and A List of Typos Made By God (http://spn-j2-bigbang.livejournal.com/232004.html) by cherie_morte

Memories of Me (http://samdean.archive.nu/series.php?seriesid=12) series by gillian

I have not read any of these. I thought I had read a lot of the amnesia fics for this fandom, I had no idea how much I was missing out on. Thank so much for your help! These all look very interesting, and I am excited to have so many good stories to start reading through. :)