The device that Non used to reconstitute Indigo's broken body is the Omegahedron, the power source for Argo City in Supergirl (1984).
Laura Vandervoort who plays Indigo also briefly portrayed Brainiac (in this series a shapeshifter) posing as Kara in Smallville (2001). In the comics, Indigo is eventually revealed to be Brainiac 8.
There was a truck which was about to collide with a car wherein Supergirl saves the family in the car. The truck's license name is PLASTINO and the logo of the truck is Plastino Chemicals. This is a direct reference to Al Plastino, who was the artist who designed Supergirl with writer Otto Binder in 1959.
Winn mentions the series Doctor Who. David Harewood, who portrays Hank Henshaw, appeared in two episodes of the popular British sci-fi series.
Fort Pemberton is named after Sylvester Pemberton, otherwise known as the Star Spangled Kid. He was a World War II superhero (part of the Golden Age of comics) and also a member of The Justice Society of America.