When Martian Manhunter enters Kara's bedroom, there is an odd stuffed toy on her bed. It resembles Zook, Martian Manhunter's comical sidekick from his 1960s comic book series.
Martha Kent says Kara (Supergirl) is out skiing with Barbara (Batgirl). In The New Batman Adventures (1997) episode Girl's Night Out (1998) it was established that Supergirl and Batgirl are friends.
The cookie J'onn takes from the plate and eats has no writing or design on it, but from its appearance is obviously an Oreo, which he is addicted to in the comics (where it's given a fake name).
Though its name and role are not mentioned, the human form J'onn takes on was the one he used in the comics as "John Jones", a police detective.
The aliens by the bar's entrance include an orange alien whose shape resembles Swamp Thing, one that could potentially be based on Marvel Comics villain M.O.D.O.K., and a robotic-bodied and a head based off of Edward G. Robinson's. Inside, two that walk in behind the two Justice League members resemble Lion Man and Hawk Man from the Flash Gordon comic strip. The latter may be an in-joke because of Hawkgirl's famous comic-book counterpart, Hawkman.