In the opening scene, when Vala (Claudia Black) says that Dr Jackson (Michael Shanks) "Doesn't look excited," Colonel Mitchell (Ben Browder) replies, "Trust me, like a kid who was up all night on Christmas Eve." Vala then replies, "I thought we imposed a moratorium on cultural references I wouldn't understand." This is a reference to Black and Browder's previous show Farscape (1999), in which Black's character was also an alien, and Browder's character was from Earth. On that show, he would constantly inundate her and the rest of the crew with Earth cultural references none of them could possibly understand.
The background music when Odyssey approaches Atlantis for the first time is a variation on the Stargate: Atlantis (2004) theme.
Ben Browder was first choice to play John Sheppard in Stargate: Atlantis (2004). Browder (Mitchell) and Joe Flanigan (Sheppard) share some scenes. Ben Browder was unable to commit to Stargate: Atlantis (2004) as he was busy filming Farscape: The Peacekeeper Wars (2004) with Claudia Black.
At 11:40, Colonel Mitchell breaks the fourth wall and looks into the camera (sharing his irritation with McKay with the viewer).