The cereal Bort is eating is called 'Greebles'. Greebles is a term used in the movie making, usually sci-fi, community to describe something added to a surface in order to make it seem more complex or interesting. It originated from Star Wars: Episode IV - A New Hope (1977) to describe structures on the exterior/interior of ships.
When Archer farts in Cyril's stasis pod, it is a call back to when Archer's cyborg clone farted in Cyril's cyborg clone's stasis pod in Deadly Velvet: Part 2 (2016).
The season's title (Archer:1999) is a parody of the syndicated '70s Sci-Fi series Space: 1999 (1975), a show that ranged anywhere between intellectual and philosophical to borderline silly and campy.
The MV Seamus patch that is visible on the right arm of Archer's uniform shirt has an ocelot on it. This is a reference to Carol/Cheryl's ocelot Baboo mentioned and shown in several previous seasons.
At one point, Pam sarcastically asks Carol/Cheryl why people rob banks; the latter answers, 'If I'm remembering this right, it's because the action is the juice.' This is a reference to a line spoken by Michael Cheritto (Tom Sizemore) in Michael Mann's Heat (1995), when he says to Neil McAuley (Robert De Niro), 'Well, for me, the action is the juice.' Again, this line is spoken in reference to bank robbery.