When the Joker shoots the robots in the "World's Fair", the sound of them winding down is the sound of the Millennium Falcon winding down from Star Wars: Episode V - The Empire Strikes Back
The chorale heard during the opening titles are actually chanting several names backwards, including the last names (at least) of production team members Alan Burnett, Eric Radomski and Bruce W. Timm.
Late in production, Warner Bros. decided to make the movie a theatrical release instead of the originally intended direct-to-video feature. This left the show's creators with less than a year of production time and scrambling to convert the aspect ratio to wide-screen.