Dead in the Desert
by liketheriver
http://community.livejournal.com/sga_details_fic/12643.html
Sympathy for the Devil
by Kristen999
http://kristen999.livejournal.com/207821.html
or
http://www.fanfiction.net/s/4764778/1/Sympathy_for_the_Devil
Solitary Man
by FanwriterWV
http://www.fanfiction.net/s/4764934/1/Solitary_Man
a story from the wraith’s point of view
Silencing the Voice (multi-chapter)
By pygmymuse
http://www.fanfiction.net/s/4672489/1/Silencing_the_Voice
An AU of this AU with John/Teyla
Move [Note: this one is being further continued so check it out again]
By Mwilalds
http://www.fanfiction.net/s/4767061/1/Move
The Chance
By glitterdash (gen, or pre-slash, however you see it)
http://glitterdash.livejournal.com/1987.html
The Genesis of John
By Arem
http://www.fanfiction.net/s/4753564/1/The_Geneses_of_John
This one involves John’s brother
Face to Face
By Rhymer23
http://rhymer23.livejournal.com/53700.html
(not a happy ending, just to warn you)
The Way It Should Have Been
By Padawan_aneiki
http://community.livejournal.com/sheps_atlantis/181949.html
ADDITIONS (culled from comments section)
Last Thoughts
by Negolith2
http://negolith2.livejournal.com/30244.html
Sous Erasure
by Harriet-spy
http://harriet-spy.livejournal.com/602255.html
NOTE: Even more links provided in comments below.