It is implied in one scene that Waylon Smither did something extremely bad at a park when Chief Wiggum was on patrol at night that his not being arrested made clear his misdemeanor of not wearing a hat in public ensured his immunity to being arrested for that ("Oh Smithers, if I didn't arrest you that night in the park, I'm not going to arrest you now..." )
The various prison scenes parody several different movies and TV shows, most notably Oz and Escape from Alcatraz.
Marge refers to Fat Tony's son as Michael, a reference to the movie The Godfather. Michael would later be seen in season 18, in the episode "The Mook, the Chef, the Wife and Her Homer".
When arresting Homer, Chief Wiggum references the television series CSI: Crime Scene Investigation.
The hat Homer wears in prison is inspired by Simon Adebisi from the Oz series.
This episode makes fun of the music of Philip Glass. When people are leaving during a piece of Beethoven Marge shouts "Wait! The next piece is an atonal medley by Philip Glass!" When she shouts this, everybody runs out of the hall, including the orchestra.
On the letter from Marge to Frank Gehry we can see an image of Snoopy. Another references to him is when Santa's Little Helper is flying a red plane in a red scarf, very much like Snoopy vs. the Red Baron. Or when Homer sleeps above a red dog house, like Snoopy usually does.
Homer is seen trying to escape from the prisoners on a Segway PT.
Frank Gehry is the first architect to appear on The Simpsons. There are several references to his unorthodox designs, such as Gehry crumpling a letter and throwing it, only to discover that it's the perfect building design.
When being asked to be the prison snitch, Homer asks if he will eat cheese and imitates Wallace from Wallace and Gromit.
The conductor of the orchestra resembles Herbert Von Karajan, a German conductor famous for his Beethoven conductings.
When Mr. Burns is reading out the list of drugs, one of them is blue bomber (which is a nickname for the video game character Mega Man).