While wearing a Carver High School T-shirt, Warren laments that he hurt his knee playing basketball, which ended his chances of playing professionally, and he dropped out of school as a result. This explains why Warren is an orderly at St. Eligius after being poised for an NBA career when he was last seen in The White Shadow (1978).
Dr Craig says "I haven't had this much fun since BJ Honeycutt and I closed the Kimchi Palace". BJ Honeycutt was one of the doctors on M*A*S*H. He therefore seems to be suggesting that St.Elsewhere & M*A*S*H exist in the same fictional universe.
The title comes from the 1965 James Brown song "Papa's Got a Brand New Bag".