The two pods on AZI-3's lower left and right look very similar to the pods of V.I.N.CENT. in 1979's movie The Black Hole.
According to Dave Filoni, from his earliest conversations with George Lucas coming onto Clone Wars, as far back as 2005 when he put to him "What was Order 66, and how did it work?", [George Lucas] was always connected to the idea that it was somewhat of a Manchurian Candidate (The Manchurian Candidate (1962)) concept. When the order goes down, it's not like the clones have a real way to say, "No, I'm not going to do this."
The 'Jedi fortune cookie' message that opens the show reads "The wise benefit from a second opinion."
Clone troopers being unwitting assassins and having dreams and nightmares of a "mission," which was mentioned by clone trooper Tup, is a reference to the movie The Manchurian Candidate (1962). In that movie, Communists brainwashed a group of U.S. troops during their captivity, turning them into unwitting assassins, who all shared the same nightmare. According to Dave Filoni, George Lucas was always connected to the idea that [Order 66] was somewhat of a Manchurian Candidate concept.