Stewie teaching Eliza to pronounce her words differently is a nod to My Fair Lady. And there is a double connection since Stewie's voice is based on Rex Harrison, the actor who portrayed the character teaching Eliza pronunciation in that property.
In the Tron sequence, the patterns on the walls of the light-cycle arena read "If you can read this your TV is upside down" - upside down.
The song Peter plays on the glasses before the hurricane is "What I Did For Love" from the musical "A Chorus Line".
The nasal-voiced character Nigel Pinchley is based on the actor
Kenneth Williams who was a fixture
of the long running British "Carry On..." comedies.
While in prison, Joe tells the others that another inmate is "so mean, he once shot a man for snoring." This is a reference to Old West outlaw John Wesley Hardin (1853-1895). On 6 Aug 1871, Hardin killed a man for snoring too loudly in the hotel room next to his. Although the actual killing was accidental (he merely intended to wake the man up), the incident earned him a reputation as a man "so mean, he once shot a man for snoring."