There's minchout's Trip-Hop Verse (http://archiveofourown.org/works/995209/chapters/1968483): "This is the story of two people who find each other and try to make it work. Featuring Bipolar!Jensen and Artist!Jared."

In From the Cold (http://archiveofourown.org/works/449210) by ladyjanelly is a gorgeous story in which Jensen suffers from amnesia: "One thing about working in a free clinic, Jared thinks, is that work is never boring. You never know what'll come in from the cold on a night like this."

Jensen suffers from amnesia in Beholder (http://sandymg.livejournal.com/37314.html) by sandymg, too, which is another story I really loved: "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."

Oh and kalliel has a wonderful story about Dean with amnesia called Here There Be Tygers (http://kalliel.livejournal.com/206457.html): "The problem with Dean's memory is, it means he asks that question about eight trillion times more ("Sammy, are you okay? well, are you?") and as far as Sam's concerned, the answer matters even less. The problem with Dean's life is, it's supposed to end this year. And the problem with Dean's brother, well. Sam's still working on that one." (this one's gen)

And of course, if you haven't read In a Mirror Distorted and Indistinct (http://archiveofourown.org/works/222249) by felisblanco, go do that IMMEDIATELY: "They keep calling him beautiful. Pretty. “Come on. Look this way. Give us a smile, Jensen.” He smiles and blinks against the flashes, fighting the urge to lower his eyes, to hide the blush burning under layers of makeup. Sweat runs down his back, his hands tremble. He’s not pretty, not beautiful. He’s small and weak and pathetic and one day they’re all gonna figure it out. One day…."

Some more lists based on your tags: amnesiac!Dean (https://delicious.com/elwarre/amnesiac!dean), homeless!Dean (https://delicious.com/elwarre/homeless!dean), homeless!Jensen (https://delicious.com/elwarre/homeless!Jensen), incarcerated!Dean (https://delicious.com/elwarre/arrested!dean), incarcerated!Jensen (https://delicious.com/elwarre/arrested!jensen), mute!Jensen (https://delicious.com/elwarre/mute!jensen).