One of the pieces of promotional artwork for the game features Guybrush Threepwood standing in front of a desert structure with a monkey's shadow projecting from him. The poster's a parody of the official teaser poster for the film Star Wars Episode I: The Phantom Menace of Anakin Skywalker in front of a structure on Tatooine with a shadow of Darth Vader projecting off of him.

In the Lucre Island Jail, if Guybrush looks at the iron maiden he'll say "Iron Maiden! Excellent!". This is a reference to the line said in the film "Bill & Ted's Excellent Adventure".

In the PC version, if you type "skull" anytime during the game, Murray the skull will appear on the screen laughing.

In the Lua Bar kitchen, there's a stove with two brass mechanical monkeys pumping its levers. If players examine them, Guybrush will say "Brass Monkey!" followed by an unseen audience shouting "That Funky Monkey!". This is a reference to the Beastie Boys song "Brass Monkey".

In Act II: Enter the Manatee, after Guybrush returns to Mêlée Island he finds out that Ozzie Mandrill has acquired the Scumm Bar and has turned it into the Lua Bar.

This is a reference to how the previous three installments used the SCUMM scripting language, which the Bar was first named after, and how Escape from Monkey Island was the first to use the Lua programming language instead.