This is an incomplete list of references to other works (games, books and films) that can be found in the computer role-playing game Deus Ex
developed by Ion Storm
Austin. The list has now been revised with additions pointed out by several noders. For more general information about the game, try looking it up on GameFAQs
Deus Ex is based in a dystopian future stitched together from elements cribbed from Blade Runner and its ilk. The protagonist, J.C. Denton, a cyborg secret agent without a past, gets embroiled in a global conspiracy which leads the player through New York, Paris and Hong Kong.
Star Wars trilogy: One of the subplots in the game involves nanotechnology-enhanced swords- the visual representation of these weapons and the scenes where they are used bear some resemblance to the lightsabre battles in the Star Wars movies.
The Abyss: The docking area for the miniature submarines seems to be modelled after one of the sets from this movie.
The Matrix: The New York subway station is similar to the one seen in this movie. The whole trenchcoat-and-shades thing is also very similar, although it should be noted that The Matrix was not released until very late in Deus Ex's development.
Ultima Underworld: The nightclub in New York is called the Underworld Club, and Underworld is used as a password. (Warren Spector worked on both games.)
Soylent Green: Candy bars located around the game world bear the slogan "Choc-o-lent Dream: It's chocolate! It's people! It's both!"
Fahrenheit 451: The first keypad code in the game is '0451'.
The Island of Dr. Moreau: The name of the scientist in the MJ-12 genetics lab ("Unknown Location") is Dr. Moreau.
Neuromancer: Several elements, the most prominent being the sentient A.I. characters (Icarus, Daedalus, etc.) draw inspiration from William Gibson's seminal cyberpunk novel.
Illuminatus! trilogy: The monologue given by Tracer Tong as you escape the VersaLife lab (about 1723 and Adam Weishaupt) is heavily influenced by the Illuminatus! books. Many elements of the game's story are based around the Illuminati / Knights Templar conspiracy theory lore. In the clinic in New York, a down-and-out greets you with the Masonic distress code "Will nobody help the widow's son?".
Gormenghast trilogy: The chef in the Paris Cathedral section is called Swelter.
Trinity: In the Area 51 bunker, there is a cryogenic storage facility where Denton finds several cloned agents. The computer attached to one of the vats gives the name 'Wade Walker' which is likely to be a reference to 'Wabe Walker', the protagonist in the Infocom adventure game Trinity who travelled through time to the scene of several nuclear explosions (which would make sense, as the Illuminati had launched a nuke at Area 51 directly before this part of the game begins).
System Shock series: There are many parallels between System Shock 1 and 2 and Deus Ex, as they shared some development staff. The AI characters in the game (Icarus, Daedalus, Helios and Morpheus) are similar to Shodan from the System Shock games. Both games also feature basketball hoops that reveal hidden messages when used.
Ion Storm (Dallas): An overheard conversation reveals the addictions of one character's "game developer friends in Dallas".
The Man Who Was Thursday: Extracts from this book are located throughout the game. The character Gabriel Syme is listed in the 'ton Hotel guest registry.
The Stars My Destination: Gully Foyle also checked in at the 'ton.
Miss Smilla's Feeling for Snow: Smilla Jasperson also stayed there.
Gravity's Rainbow: ...as did Oberst Enzian.
Sandman: ...as did Hippolyta Hall.
The Diamond Age: Gunther Hermann makes a request in an email message to have a gun implanted in his skull (a somewhat pointless technology described in the opening chapter of Neal Stephenson's novel).
Special thanks to the network of clandestine operatives who have contributed to this writeup.