The shot of Superman holding an unconscious Supergirl in his arms recreates and pays homage to the famous cover of "Crisis on Infinite Earths" #7, published in 1985, in which Supergirl saves her fellow heroes, resulting in her death.
When Schott locates a source for Promethium, a chemical formula is shown on his display -- C12H22O11. This is the formula for common table sugar.
In Silver Age comic books, Snapper Carr was the teenaged "mascot" of The Justice League of America.
Alex mentions giving up a medical career to work at the DEO, a possible nod to her role as Dr. Lexie Grey in Grey's Anatomy (2005).
At 7:40 Cat Grant pronounces Kara's name correctly for the second time in the series. The first was at the conclusion of season 1 when Cat moved Kara into her own office.