I've been thinking about this post and all I can do is list the fics that have knocked my socks off vs. the character study b/c Sholio beat me to most of them.
Sholio
Title: Candle in the Dark http://www.fanfiction.net/s/3036654/1/
Title: Ghost in the Machine http://www.fanfiction.net/s/3214884/1/Ghost_in_the_Machine
Title:Between the Lines http://community.livejournal.com/sga_flashfic/642838.html
sazz27
Title:Nothing But Sky http://www.fanfiction.net/s/3160849/1/
Stealth Dragon
Title:Of Coloring Books and Lt Colonels
Kodiakbear
Title: And the Sky was Dark http://www.fanfiction.net/s/2767929/1/And_the_Sky_was_Dark
Baroqy
Title:Devotio Moderna http://www.fanfiction.net/s/3425857/1/Devotio_Moderna
skypig21
Title:The Known World http://www.fanfiction.net/s/3300672/1/The_Known_World
liketheriver
Title:So Little Space, So Much Time http://liketheriverrun.livejournal.com/6240.html#cutid1
There are others but these are some of the best written I know.
no subject
Sholio
Title: Candle in the Dark
http://www.fanfiction.net/s/3036654/1/
Title: Ghost in the Machine
http://www.fanfiction.net/s/3214884/1/Ghost_in_the_Machine
Title:Between the Lines
http://community.livejournal.com/sga_flashfic/642838.html
sazz27
Title:Nothing But Sky
http://www.fanfiction.net/s/3160849/1/
Stealth Dragon
Title:Of Coloring Books and Lt Colonels
Kodiakbear
Title: And the Sky was Dark
http://www.fanfiction.net/s/2767929/1/And_the_Sky_was_Dark
Baroqy
Title:Devotio Moderna
http://www.fanfiction.net/s/3425857/1/Devotio_Moderna
skypig21
Title:The Known World
http://www.fanfiction.net/s/3300672/1/The_Known_World
liketheriver
Title:So Little Space, So Much Time
http://liketheriverrun.livejournal.com/6240.html#cutid1
There are others but these are some of the best written I know.