I can self-rec a few. :D
2.)War is Never Cheap, Dear (http://quickreaver.livejournal.com/39662.html)
6.)In The Blood Red Dust (http://quickreaver.livejournal.com/51855.html)

Also, monicawoe has some great gen dark!fics that don't necessarily end with mass murder!

If I think of any others, I'll post 'em. Enjoy!

Possession

Passenger & Sequels
Dean is possessed. Unpleasantness ensues.
http://kroki-refur.livejournal.com/191753.html

Fade To Black
Roosevelt Asylum was Chicken Soup for a Brother's Soul. Compared to this.
http://phx69.livejournal.com/34841.html

AU

Here at the end of all things (you have to register to read, it takes 2 minutes, but this story is worth it if you're not already a member)
Who will be left standing at the end of it all... Set at the end of the final season and beyond
http://supernaturalville.net/viewstory.php?skin=Zenlike&sid=3009&chapter=1&textsize=6

I've a Delicious account it has word count tags if you're interested ..............

http://previous.delicious.com/chellexxx1/SPN+Gen

xxx

This verse fits all your requests except 5/

Angelwings by leonidsalion http://archiveofourown.org/series/6229 (word count 178,258)

Dust Devils (http://www.fanfiction.net/s/8060551/1/Dust-Devils) by Sharlot (check out her other stories as well, she's awesome)

6#
Skinwalker!Dean series by liliaeth
archiveofourown.org/series/15418

Skinwalker are not only born as this, they can change a human by bitting. Dean was bitten as a child.

2# + 6#
Bring the Rain by sinestrated
sinestrated.livejournal.com/52944.html

Jared and Jensen are orphran. To take care of Jared, Jensen sells his body and memories to the military.

#1 & 6 - The Fusion verse by ratherastory.
Summary: Dean fucks up his knee one too many times and either has to amputate or fuse it, so he chooses to have it fused. He can walk with little-to-no pain, but he underestimated how incredibly frustrating it is to have a permanently unbendable leg -- everything is a challenge; sitting, climbing stairs, getting comfortable in bed, and he can't even drive.
http://archiveofourown.org/series/8645 (http://archiveofourown.org/series/8645)

# 5 - While You Were In College by staceycj. Summary: Dean learned to do some interesting things while Sam was at Stanford.
http://www.fanfiction.net/s/5752200/1/While-You-Were-In-College (http://www.fanfiction.net/s/5752200/1/While-You-Were-In-College)

Bound Together
http://emeralds75.livejournal.com/3985.html