On the bus when Kara opens the first comic book given to her by Clark, she says "Spider powers? Ew!" This is a light jab at Spider-Man.
When describing how a baseball team made her their honorary "batgirl", Supergirl pretty much tells the Kent's Barbara Gordon's dual identity.
Unlike in the comic books, in this episode, for some reason, Superman needs to use use a microscope first before he can utilize his microscopic vision.
The cat seen on Supergirl's bed at the beginning of the show is meant to look like Streaky, a cat Supergirl had in the comics that was orange with a white lightning bolt pattern on its sides! The cat is in fact named Streaky as Kara calls her by name in this story.