When Johnny discusses going "legit" with Lil, they happily envision all the wonderful things offered by such a lifestyle. One of the benefits was the ability to "say 'hi' to a neighbor named Fred", a tip of the hat to Fred Rogers. Michael Keaton got started in the industry by working as a stagehand on Mister Rogers' Neighborhood (1968) when he was still living in Pittsburgh. When Rogers died in 2003, Keaton hosted Fred Rogers: America's Favorite Neighbor (2004), a memorial program on PBS dedicated to his friend and mentor.
The "cozy little love nest" the District Attorney offers Tommy is actually the Philadelphia Museum of Art.
The newspaper photo of D.A. Burr is actually of Louie DePalma from Taxi (1978). It was also used for character "Frank Stedman" in Head Office (1985).
Michael Keaton's characterization of Johnny Dangerously frequently spoofs James Cagney, a star of gangster movies from the golden age of old Hollywood.
Brian De Palma is a massive fan of the film. He reportedly laughed hysterically throughout an advance screening. Two months after its release, De Palma cast Danny DeVito and Joe Piscopo in his next project, Wise Guys (1986), another Mafia-themed comedy.