Bill Lawrence and a few of the writers jokingly claim that Neil Flynn (The Janitor) has never actually spoken a line from any script. A fourth season script reportedly even contained "(Whatever Neil says)". While Lawrence's comment is certainly an exaggeration, it illustrates how much of his performance is spontaneous.
Dr. Cox's (John C. McGinley's) trademark of calling J.D. by girls' names is what McGinley does in real life (jokingly) to his good friend and neighbor, John Cusack.
Every episode was scripted, but the actors had the choice to improvise their lines if they thought of something funnier.
Ted's (Sam Lloyd's) "band" is "The Blanks", a group Lloyd formed with his friends at college.
It was Zach Braff who suggested using the song "Superman" by Lazlo Bane as the show's theme after listening to the lyrics and finding them in mood with the pilot.