When Toyman is choosing Wonder Woman, her costume changes from every version of Wonder Woman's costume through the years, from Cathy Lee Crosby to the different versions of Lynda Carter's.
The enlarging 'S' shield that Superman throws at Batman is a reference to the same unexplained power the character uses in the 1981 film, "Superman II" (which is why the Cyborg complains, "Hey, Superman can't do that!").
When Superman flies straight up in the air during the game, you can faintly hear the John Williams' Superman theme.