When Lex leaves prison, he leaves a hologram of himself, just like it was done in Superman II (1980).
At one point when going under cover, Snowbird is seen disguising herself with a brown haired wig and using the alias Linda Lee. In the comics, Supergirl's original secret identity was Linda Lee and she hid her true identity by wearing a brown haired wig.
When Eve confronts Snowbird at L-Corp, she mentions Philip Jennings, the deep-cover KGB operative played by Matthew Rhys in The Americans (2013).
The title is a play on the House of El, Kara and Clark's biological family on Krypton.
It is mentioned that Lex was named after Alexander the Great, a reference from the comic books.