In the comics, Rama Khan is not an alien but a human, or more rather a homo magi (a sub-race of naturally magic-wielding humans that evolved in a parallel but separate line, alongside homo sapiens). He lived 3,000 years ago as the ruler of the nation of Jarhanpur. He later became the joint ruler of ancient Atlantis.
When Kara invites her to the Fortress of Solitude, Lena ponders the ramifications of a Luthor's presence there. Lex has previously found his way into the Fortress in Superman II (1980), Superman Returns (2006), and the seventh-season finale of Smallville (2001).
The old woman from the Leviathan organization is referred to as "Margot". This is likely a direct reference (and homage) to Margot Kidder, the actress who portrayed Lois Lane in the Superman movie quadrilogy (1978-1987).
When Kara tells Lena about the Fortress of Solitude, she says that Superman created it. In the comics, The Fortress was created by The Eradicator, an ancient Kryptonian artifact that was built to preserve all Kryptonian life forms by eradicating anything that posed a threat to Kryptonians. The Eradicator was gifted to Superman and brought to Earth where it built the Fortress of Solitude by reshaping the ice in the arctic and opening a portal to the Phantom Zone to filch Kryptonian technology directly to the fortress. Eventually the Eradicator became sentient and took on a humanoid body to fight Superman because the Eradicator felt Kal-el stood in opposition to Kryptonian ideals, only to be defeated. In the wake of the "Death of Superman" comics, however, he would become vastly more important to Kal-el's story.
Mitch Pileggi, playing Rama Khan, was on several episodes of "Supernatural" which also featured an arc about Leviathan for a season.