Remember the fetus Mulder finds in Emily that's labeled with Scully's name? These are stories that deal with what happens to it.
Cotton Wool by Neoxphile WIP
Five Years & One Night by Shalimar
Erlenmeyer Injustice by Pattie
Cloned Injustice by Pattie
Eugenic Injustice by Pattie
Sarrah by Jessica Hildbold
Misbegotten Sons by Neoxphile (coming in 2010)
There's a Nursery Files challenge on this topic too, so if you'd like to write a fic about what happens to that darn fetus go here for challenge details.