At the end of the weekly meeting of the Justice League, Cyborg says, "All right, well, if that's it, we'll meet next Thursday. Same Bat time, same Bat channel." This is a sly reference to the old 1966-68 TV series "Batman (1966)," which used the "Same Bat time, same Bat channel" phrase as a slogan at the end of each episode to promote the next episode.
At one point during Superman's battle with Doomsday, as Superman is weakening, Lois Lane says, "Don't worry, I've got you" and Superman replies, "You've got me? Who's got you?" This is a reversed tribute to the same lines in the Christopher Reeve/Margot Kidder film "Superman (1978)," in which the same lines are spoken, but by the opposite characters.