When the group first meets Roy he says "It's ok to be confused, many new arrivals are. We had a guy from Riverside, Iowa show up, thought he was a starship captain". Riverside, Iowa is the birthplace of the Star Trek (1966) character James T. Kirk, captain of the starship Enterprise.
Several references to The X-Files (1993) including the character name Dan Scully; Gillian Anderson's character in The X Files was called Dana Scully.
Missi Pyle who plays Bernadette in episode Rozwell, is also known for playing an alien character in the movie Galaxy Quest.
"Don't you think it's unusual that these aliens mostly communicate in English.... mostly." Is a reference to the movie Aliens.
The character Bernadette may be a reference to Saint Bernadette who had visions including white lights.