When Bruce is checking the future Joker's voice-print against that of the past Joker's, the clip is a newly animated (but previously scripted) segment from Holiday Knights (1997), which was the first episode produced of The New Batman Adventures (1997).
When Terry lists possible explanations for the Joker's return, he mentions being in "Suspended animation after being found frozen in a block of ice." This is a reference to the Marvel Comics character Captain America, who was found in an identical state by the Avengers in the 1960s.
The orbital weapons platform that creates a beam of light before it destroys something is taken from the 1988 Japanese animated film Akira (1988), as is the basic design for the orbital weapons platform itself. In fact, one of the directors of animation at Tokyo Movie Shinsa (the Japanese animation company where most of the film was made) was the actual animator of the scene in Akira (1988) when Kaneda was briefly chased by the beam from the orbital system. When the scene of Terry being chased by the beam came up, the director snagged the storyboarding duties on it for himself under the auspices of aiming to top himself.
The voice of Ghoul was provided by Michael Rosenbaum, who did several voices for the TV series Batman Beyond (1999). While in the recording studio, he would often do a Christopher Walken impression that the producers thought was hilarious. When they were commissioned to create this film, they wrote the part of Ghoul for Rosenbaum's Walken impression. He would later reprise the role of Ghoul in the Justice League Unlimited (2004) episode The Once and Future Thing, Part Two: Time, Warped (2005).
The abandoned Jolly Jack Candy Factory that the resurrected Joker uses as a hideout in the film is named for legendary comics artist Jack Kirby, who was known as "Jolly" Jack Kirby early in his career.