There is a technology shop in Prague named "Tech Noir"; a reference to The Terminator. This is the name of the nightclub that Sarah Connor first encounters Kyle Reese and The Terminator in. Additionally, tech-noir is considered a hybrid genre of traditional film-noir and science fiction/cyberpunk themes. This is a more than fitting description of the Deus Ex universe/game series.
In Elias Chikane's safe in the puppet workshop a pocket secretary can be found. It contains the coordinates 47°22'n 8°33'e. These coordinates are located in Zurich, Switzerland.
In Prague, near the Bolzano Monument, there is a merchant shop named "Sobchak Security". This is a nod to the business of the same name, owned by the character Walter Sobchak in the film The Big Lebowski.
In the basement of the "Future-Past Antiky" shop in Prague, several video game boxes of previous Eidos games, such as Soul Reaver, Tomb Raider and Hitman are visible.
Adam Jensen is the only character in the series to be featured in 2 games, as the main protagonist.