In the flashback of his first day with Lois at the Daily Planet, the Nazi symbol that Clark mistakes for lightning bolts, which are actually stylized S's, is the rune used by the Schutzstaffel, the Nazis' security agency. The symbol also appeared, in place of the House of El glyph, on the suit of Overgirl, the parallel-Earth counterpart of his cousin Kara, in the "Crisis on Earth-X" crossover.
Clark watching reruns of Seinfeld (1989) is an homage to Jerry Seinfeld being a Superman fan; in "The Race (1994)", Jerry even dates a woman named Lois.
Jor-El's words to his son Kal-El/Clark/Superman before Superman's first flight mirrors Man of Steel (2013), including his excitement about his own first flight.
Henry Miller's villainous name is given as "Atom-Man" in the end credits. Atom Man, aka Lex Luthor, was the villain that Superman fought in the 1950 serial Atom Man vs. Superman (1950).
A teenage Morgan Edge tells Zeta-Ro the year is 1987, the same year that Tyler Hoechlin was born.