When Megabyte betrays the CPUs, Binky cries "It's the ABC's! They've turned on us! Treacherous Dogs!", an in-joke towards the ABC Network for not renewing ReBoot for the third season and dropping the show completely from its show line-up.
The subway station "Piccadilly Circuits" is a pun of the British underground "Piccadilly Circus Tube Station" in London. The Binomes seeking refuge there is a reference to Londoners using the stations as bomb shelters during the 1940s World War II Blitz.
One of the police cars flying has the number A12 in reference to the tv show Adam 12