Michael Arndt won for best original screenplay for "Little Miss Sunshine," and William Monahan won for best adapted screenplay for "The Departed."
Both films are nominated for Oscars for writing as well as best picture.
Amy Berg won for best documentary screenplay for "Deliver Us from Evil," an account of sexual abuse by Roman Catholic priests.
HBO's "The Sopranos" was honored for TV dramatic series writing, and NBC's "The Office" took the award for best comedy series.
ABC's "Ugly Betty" won for best new series, and Fox's "The Simpsons" won for animation.
The awards were presented in dual ceremonies in Los Angeles and New York.