well thats not hard considering that the main character of so many stories out there (not just anime) ate orphans because for some weird reason its extremely popluar to have main characters without parents...
*sigh* Well, technically L's dad died although we never saw him.. because L was an orphan so his parents must've died. Also, Watari was kind of like a father and he died... D:
Nina Tucker in Fullmetal Alchemist Brotherhood.
After she and her dog were made into a pained monster by her father, Scar eventually arrived and killed him, he then gave Nina a mercy kill.