If you have a really strong stomach, there's a fairly new story on FanFiction Net by kiku65 called "Thanatos". Good plot but very upsetting torture. And it's a WIP, though it's updated regularly.
If you're looking for slash, Wing and a Prayer (http://the-cephalopod.livejournal.com/19981.html) by sgamadison and the_cephalopod has a tortured John.
A gen-story revolving around a tortured John: "The Mercy Variant" and "What Wrongs thee has wrought" (http://kodiak-bear.livejournal.com/137190.html) by kodiak_bear. AFAIK Sholio also wrote a sequel to that.
My story One Piece At A Time (http://argosy.livejournal.com/70281.html) has, amongst many other things, offscreen Sheppard imprisonment and torture. But I'm here to point you to the fantastic remix by cupidsbow, One Peace At A Time (http://cupidsbow.livejournal.com/282801.html) that expands on the captivity and torture.
Stealthdragon's always my go-to torture writer--Castles in the Sky is fantastic if slightly unconventional torture: http://www.fanfiction.net/s/3806338/1/Castles_in_the_Sky Mercy has some great high tech torture: http://www.fanfiction.net/s/2879952/1/Mercy
and there's the often ignored Uncommon Alliance by Stargalaxy: http://www.fanfiction.net/s/3366713/1/Uncommon_Alliance All 3 are gen and ridiculously long :) Titan5 also has a couple of shorter pieces on ff.net Infirmary nightmares: http://www.fanfiction.net/s/3201973/1/Infirmary_Nightmares (with flashback torture) The Problem with Good Deeds: http://www.fanfiction.net/s/3309142/1/The_Problem_with_Good_Deeds
I'd post the stories individually, but the list's too long. http://del.icio.us/splitbeak/sheppard+torture (http://del.icio.us/splitbeak/sheppard+torture)
no subject
Date: 2008-07-24 04:34 am (UTC)no subject
Date: 2008-07-24 06:35 am (UTC)http://www.fanfiction.net/s/3018384/1/Its_Always_Autumn_in_the_Old_Trees_of_Despair
Two of the most fantastic fics ever written!
no subject
Date: 2008-07-24 07:58 am (UTC)A gen-story revolving around a tortured John: "The Mercy Variant" and "What Wrongs thee has wrought" (http://kodiak-bear.livejournal.com/137190.html) by
no subject
Date: 2008-07-24 08:22 am (UTC)no subject
Date: 2008-07-24 11:34 am (UTC)In Children's Classics by taste_is_sweet both John and Rodney suffer, iirc, it's also slash.
Helpless by kriadydragon is gen with Sheppard and Ronon, and Sheppard being tortured.
no subject
Date: 2008-07-24 12:06 pm (UTC)Mercy has some great high tech torture: http://www.fanfiction.net/s/2879952/1/Mercy
and there's the often ignored Uncommon Alliance by Stargalaxy: http://www.fanfiction.net/s/3366713/1/Uncommon_Alliance
All 3 are gen and ridiculously long :)
Titan5 also has a couple of shorter pieces on ff.net
Infirmary nightmares: http://www.fanfiction.net/s/3201973/1/Infirmary_Nightmares (with flashback torture)
The Problem with Good Deeds: http://www.fanfiction.net/s/3309142/1/The_Problem_with_Good_Deeds
Hope those help!
no subject
Date: 2008-07-24 12:49 pm (UTC)no subject
Date: 2008-07-25 01:52 am (UTC)