Doom 3 includes several references to the original Doom:
- At the start of the game, the player can access a communal area where there is an arcade machine named Super Turbo Turkey Puncher 3. The game is formed mostly from Doom graphics, and features the fist, status bar face, gibs and a background which is clearly a screenshot from E4M9 of Ultimate Doom. The game logo alludes to Street Fighter Alpha 3 and the fictional developer Nabcon to Capcom.
- A texture that was ported from parts of Doom 1 computer textures, is used at several points, mostly used in the CPU banks. It comes mostly from COMP2 and COMPTALL.
- Throughout the game, magazines can be found in the Mars base. One of these, GameHOG, features the status bar "ouch face" blown up to fill the front cover, as well as the title of a fictitious game Doom Ultra-XL.
- The original cheat codes, when typed at the console, will cause the message "your memory serves you well!" to be displayed telling you that you know your DOOM skills.
- The light patterns in the pentagrams found in hell include a small image of the original status bar face. The pentagrams also feature the UAC logo.
- One of the rock images at Site 3 features the box cover picture of the original Doom, slightly modified so that the player is carrying a Doom 3-specific weapon.
- When sending a message to the fleet, the computer screen includes the code "IDSPISPOPD", one of the classic cheat codes.
- The sound of picking up an access card is the same as Doom's item pickup sound.
- One of the PDAs available in the main campaign belongs to a "Robert Price". This is possibly an intentional misspelling of Robert Prince, id's composer between 1991 and 1994.
- In Resurrection of Evil, one of the minigames, Martianbuddy Blaster, features the sprite of the classic BFG9000.
- In the Monorail level, it's possible to witness a picture of a Zombieman. This is possible by activating the noclip cheat and moving to the cinematic area where Betruger transforms a marine. The picture is located on one of the glass panels.