The hypnotism code word "Nero" refers to Emperor Nero, who was said to have played the violin while the city of Rome was on fire and that he may have started the fire on purpose. Nero is also the name of the vice principal of Prufrock Preparatory School in The Austere Academy. Vice Principal Nero's silhouette playing the violin is shown at the end of the episode.
During a confrontation towards the end, Count Olaf asks Violet if she hasn't learned anything during this "year.. week.. season." Season here is a subtle form to break the fourth wall.
Georgina Orwell, the optometrist, is named after George Orwell. He wrote 1984, a novel about the government always watching citizens and giving them no privacy.
When the Baudelaires sneak into Dr. Georgina Orwell's office and Count Olaf hears something above him, he says "If there's nothing up there then what was that noise?" This almost completely mirrors the V.F.D recruitment saying where an individual, as a child, asks if there is something outside; if the parents reply "nothing," this is code and the individual must respond with "If there's nothing out there, then what was that noise?"
During the opening theme song; the owner of the mill's face is never shown, except from behind or covered in a cloud of cigar smoke. This is a reference to the "Miserable Mill" book where this character never has his face seen by anyone, but is always described by having a thick cloud of smoke covering his head.