The diction used in the sewer-people's laws are based on that of the animal-men on the Island of Doctor Moreau. I.e., beginning with 'Always to' or 'Not to' (e.g. 'Always to wash hands and face' or 'Not to go on all-fours').
The subliminal flashes of a pixelated demon face alternating with the image of M.U.T.H.E.R, during Dr Orpheus's scrying through the shelter's wall references the film.
Dr Venture also encounters a man resembling Booji Boy, as well as the under-dwellers leader, who resembles General Boy, both characters from Devo's "Jocko Homo" music video.
The computer program M.U.T.H.E.R , as well as the under-dwellers worshipping Dr Venture's dad as "Father" are likely references to MU/TH/UR 6000 & FATHER, two super computer systems used in the Alien franchise.
In the tunnels, there is a man dressed as Trevor Horn of The Buggles as he appears in the music video for "Video Killed the Radio Star". Dr Venture comments on this by asking, "Is that the guy from The Buggles?