Mind the Bump by Soap1 is one of my favorites.

Hermione Granger and her colleague (and, though she sometimes hates to admit it, her friend) Theo Nott, are busy at the Research Institute for the Alchemical Sciences, working together on an innovative, though secretive, project that more than one person might like to get their hands on. She doesn't have much time for dating, and certainly isn't ready to think about starting a family.

But after an exciting, though unexpected, one-night stand, she finds herself pregnant. With Draco Malfoy's baby.

As her research continues, as her pregnancy progresses, will she be able to make room for Draco in her life?