When The Joker is attacking Metropolis in the Lex-Wing, he takes a moment to maneuver in front of the moon, using it as a backdrop to the "grin" of the aircraft. This is a parody of the Bat-Wing doing the same to create a bat-signal image in Batman (1989)
After Batman and Superman destroy the robot that Mercy Graves is attached to, she proceeds to tell them that Joker took Lex Luthor in the "Lex-Wing". This may be a subtle nod to the "X-Wing" in Star Wars. Mark Hamill who voices the Joker played Luke Skywalker who piloted an X-Wing in the original Star Wars trilogy.
Harley's bag is thought by some to be a reference to Watchmen, but this is unlikely as the Watchmen graphic novel, while still in print, had not gone Mainstream by the time this episode aired. More than likely, Harley's bag (and Joker's yo-yo) were just references to the generic "Smiley" face that had been a part of pop culture since the 60's.
One of the few S: TAS storylines which feature dialog and plot points taken from the comic books; Post-Crisis.