The fact that Mr. Krabs hid the boots under the floor of the Krusty Krab, and his guilt over taking the boots being manifested as hallucinating that he hears the boots squeak, is a reference to 'Edgar Allen Poe (I)''s short story "The Tell Tale Heart". In "The Tell Tale Heart", a servant murders his master and hides the body under the floorboards. Wrought with guilt, the servant hallucinates that he can hear the master's heart beating persistently, which drives him to confess to the murder. In fact, the way Mr. Krabs confesses to stealing the boots is similar to the servant's confession in the story. Mr. Krabs says, "I did it! I took the boots! They're here! Under the floorboard! Oh, please, make it stop! It's the squeaking of the hideous boots!" a line which is akin to one the servant had: "I admit the deed!--tear up the planks!--here, here!--it is the beating of his hideous heart!"
Squeaky Boots spoofs Poe's short story "The Telltale Heart," as Mr. Krabs' conscience tortures him into revealing that he hid the boots under the floorboards, and he yells "It's the squeaking of the hideous boots!"
When SpongeBob and Patrick are first floating in zero gravity, a book floats by with "2001" written on the cover, an obvious nod to 2001 - Odyssee im Weltraum (1968).
This episode initially aired during a "Smell-o-Vision" programming gimmick, in which scratch-and-sniff cards were given in cereal boxes and Lunchables. Whenever a "nose" symbol appeared on screen, it would encourage viewers to scratch and sniff whatever was on screen.
During "Squeaky Boots", when SpongeBob first appears dropping in on Mr. Krabs in his office, Mr. Krabs refers to him as "SpongeBoy me Bob!" This could possibly be a reference to the show's original title, "SpongeBoy Ahoy!"