While in Flash's body, Lex Luthor threatens a technician's life by promising to vibrate his fingers into the man's brain. In the Flash comic #275 (July 1979), Iris Allen (the wife of the Barry Allen version of the Flash) loses her life when the villain (the Reverse-Flash) does exactly that to her.
According to the director's commentary, the writers and director had long anticipated a chance to have a joke about Luthor about to stumble onto a Justice League member's secret identity, only for it to backfire when he didn't recognize the person's face.
When the Flash and Lex switch bodies, The Flash is speaking as Lex. Michael Rosenbaum, who voices The Flash, starred in Smallville (2001) as Lex Luthor. During the scene where Flash (in Luthor's body) is in the restroom, he speaks to Dr. Polaris, also voiced by Rosenbaum.
One of The Flash/Wally West's memories Dr. Fate sees is of him running on a treadmill, a reference to his predecessor Barry Allen's invention the Cosmic Treadmill.
Early in the script, Flash was going to jokingly drop the name "the Legion of Doom". However, the line was removed before it went in for recording by request of DC Comics.