I've found less than a handful of stories.

There's one set during Common Ground, "Simple Truths" by sylvanwitch:
http://community.livejournal.com/sheppard_hc/27978.html
http://community.livejournal.com/sheppard_hc/28183.html

slippery_fish wrote me a Todd/Sheppard drabble/ficlet for Christmas:
http://slippery-fish.livejournal.com/1295214.html

Then there's one by eleveninches called "Wraith No More":
http://eleveninches.livejournal.com/323073.html

And my own, "If We Make It Past the Judgement":
http://sandrine.livejournal.com/699268.html

There needs to be more Todd/Sheppard fic. (Or Todd fic in general.) Well, maybe after next week's episode...