Emotionally, the scene in Evolution with Mara and Jude on the dock. Everything about it was horrible--Mara being forced to hurt herself to protect her family, and knowing they wouldn't believe her if she told them the truth about what happened. I find the idea of that really terrifying--the isolation of it, and the hopelessness.
It was tough for a bunch of reasons, but the simplest is that action is difficult for me to write. I have a hard time remembering where the characters' bodies are in space. (Which is one reason the climaxes in my books involve people standing around and talking instead of running at each other with swords and stuff.)