Since it seems there has been some difficulty in locating good Micheal/Sara fic, I thought I would rec some of my favorites. They are both by foxxcub, and they are fantastic. Here they are:

Forty-Seven (http://prisonbreakfic.com/viewstory.php?sid=32)

Pause (http://prisonbreakfic.com/viewstory.php?sid=33&warning=NC-17)

Also, Drowned (http://prisonbreakfic.com/viewstory.php?sid=4) and its sequel Broken (http://prisonbreakfic.com/viewstory.php?sid=5) by tinamishi are both really great M/S.