While dictating his novel, Dr. Craig says, "Put roses on the piano and tulips on the organ." This is a sneaky (and naughty) choice of words, but, after all, John Doe does say it's supposed to be pulp fiction.
Other randy bits include Dr. Craig referring to someone's girlfriend named Constance Lingus, as well as a patient named "Pat" McGroyn.
Resident Griffin makes at least three entertainment puns early on. He says, "Sunday, Bloody Sunday", a 1983 song by U2. He also cautions, "No, no, Nanette", the name of an early 20th century Broadway play and later musical comedy. He finishes with "Can't get no traction, Satis", an obvious pun on The Rolling Stones' 1965 classic line, "Can't get no satisfaction". Incidentally, the nurse's name is Nanette Satis.