The newspaper photo of D.A. Burr (Danny DeVito), is actually one of DeVito's character Louie DePalma from the television show Taxi (1978), and was also used for character "Frank Stedman", also played by Danny Devito, in Head Office (1985).
While the movie sends up classic gangster movies in general, the basic plot point of Johnny and Tommy Kelly ending up on opposite sides of the law is inspired by Manhattan Melodrama (1934). In that film, William Powell and Clark Gable portrayed orphans who are raised together as brothers. Clark Gable's character "Blackie Gallagher" grows up to become a gangster, while William Powell's character Jim Wade becomes a crusading District Attorney (just like Johnny and Tommy, respectively). Also, in both films, the gangster brother roots for the District Attorney brother to succeed.
The closing credits jokingly bill two writers, Neal Israel and Pat Proft, who did not co-write the movie, as "Special Medical Advisers". Neal Israel, also a director, was the second husband of Director Amy Heckerling, and were married around the time that this movie was made and released.
When Johnny discusses going "legit" with Lil, they happily envision all the wonderful things offered by such a lifestyle. One of the benefits cited by Johnny was the ability to "say 'hi' to a neighbor named Fred". This was a tip of the hat to Fred Rogers, as Michael Keaton got started in the industry by working as a stagehand on Mister Rogers' Neighborhood (1968), when he was a young man still living in his native Pittsburgh. So close was their friendship, that, when Fred Rogers died in 2003, Michael Keaton hosted a memorial program on PBS dedicated to his friend and mentor.
The rival crime boss in this film is named Maroni, a named shared by a major crime boss in the Batman universe. Michael Keaton appeared on-screen as the Caped Crusader in Batman (1989) and Batman Returns (1992).
Rival gangster Maroni's butchering of the English language is a parody of the stereotypes of Italian immigrants in old movies who have exaggerated accents and speak poor English. The parody is carried further still whenever Maroni swears.
The "Film Yearbook Volume 4" said that this movie was a "parody burlesque of Warner Brothers gangster films". This movie, ironically though, wasn't made at Warner Brothers, it was made at 20th Century Fox.