There's also a reference to a scene in Annie Hall where McLuhan castigates a film goer for misunderstanding his oeuvre.
The scene in which Brian is carefully lowered from the ceiling to steal the record without waking Peter is a reference to the film Mission: Impossible which is, in turn, based on a scene in the film Topkapi.
The scene were Stewie and Brian smash the records is a reference to the film Office Space. Where the same song, "Still" by Geto Boys plays.
Jesus said that the invasion of the church and killing of the priest is the same as in Tears of the Sun.
The scene where Stewie is on the couch with Brian is a reference to the film Cloverfield, in which the character Marlena has a bloody nose and says, "I don't feel so good."
The scene where Tom Tucker talks about Jesus' arrest is a reference to Mel Gibson's DUI arrest and the anti-Semitic comments he made.
The NY Post headline "Jesus Bigger Than Jesus" is a reference to when John Lennon was controversially quoted as saying that The Beatles were bigger than Jesus.
A badge can be seen on the wall of the 1950s restaurant saying "I like Ike". This is a reference to the campaign of ex-President Dwight D. Eisenhower.
In the song "Me and Jesus", Jesus says the line "you ain't never had a friend like me," which is a reference to the song of the same name from the 1992 Disney film Aladdin. Also, Jesus is shown riding on top of a bomb falling away from the frame, which is a reference to the film Dr. Strangelove. Peter rides a bicycle with Jesus huddled in a basket just like the film E.T. the Extra-Terrestrial.