Sally from the Mothership Zeta DLC makes references to a fictional pre-war show called 'Captain Cosmos', which itself features classic Star Trek references, such as "All systems normal, Captain!" and "Captain on the bridge!"

She also mentions a female 2nd officer, saying "Stella Skyfire reporting for duty! She's Captain Cosmos' second in command, at least for the first few episodes..."
This is in reference to the original, unaired pilot episode of Star Trek: The Original Series, "The Cage", in which Captain Pike has a female lieutenant who is second-in-command, simply referred to as "Number One". NBC rejected this pilot and requested a new pilot episode, ultimately making her role as second officer last for only one episode.

Another notable reference is the time slot 'Captain Cosmos' airs at, which was Thursdays at 8:00PM EST, according to leftover posters in the Hubris Comics building. Star Trek:ToS aired on the same day but at 8:30PM EST.