In Alpha Labs, Sector 1, Jack T. Smith's PDA can be found containing an email with the subject line "Buddy system?!". In the email, Smith complains about a newly-implemented buddy system by the UAC corporation in response to industrial accidents. A victim, Joe Moss, is referred to by the nickname "TorsoBoy" because his arms and legs were severed by the "Albuquerck Capacitator". Both his nickname and the name of the machine are references to the lyrics of the song "Albuquerque" by comedy musician "Weird Al" Yankovic.

In the original release of the Resurrection of Evil expansion pack, in a lounge area found in Level 4: Erebus Control, you can play a minigame on an arcade cabinet called "Hellanoid", a clone of the 1986 Taito game Arkanoid. A broken Hellanoid cabinet can also be found earlier in the level. There are only five layouts for each of the game's levels and they repeat in a loop with a gradually faster ball. Notably, two of the layouts are arranged into unique pictures. The picture in Level 4 is that of an Imp's face, while the picture in Level 3 is a depiction of a widely-circulated shock image hosted on the website "goatse.cx" showing a hunched-over male pornographic model stretching his anus open. In Doom 3: BFG Edition and all releases of the game since, Hellanoid was replaced with Super Turbo Turkey 3, a minigame featured in the base game.

In 2002, the alpha version of Doom 3 had been leaked online. In this alpha version, the logo used for Doom 3 looked markedly different from its final version, using stylized roman numerals like one of its predecessors Doom II: Hell on Earth.

Throughout the game, there are arcade cabinets which the player can interact with. The game is called "Super Turbo Turkey Puncher 3". This game has players to punch a turkey until it is gibbed, the graphics in the game are taken from the first 2 Doom games including the fist sprites and the background being a door from E4M9 "Fear", the fourth secret level of Doom. The title graphic is a parody of Street Fighter Alpha 3 and the company responsible for the game is "Nabcon", being a parody of Capcom.

Getting a high score on this game results in the player getting a congratulatory email which also informs the protagonist that his vacation has been docked two days for time-wasting.

In the PC version of the game, should the player attempt to input any of the original Doom or Doom II classic cheat codes (IDDQD, IDKFA etc.) into the game's console, the console will print out a message saying "Your memory serves you well!" This otherwise has no beneficial effect for the player.

In Resurrection of Evil, the playable arcade game "Martian Buddy Blaster" features the player-sprite of the BFG9000 from previous Doom titles.

The marine in Doom 3, while unnamed in the game, is called John Kane in the Doom 3 novel Worlds on Fire.

In the chapter "Site 3", one of the stone tablets represents the cover of the original Doom.

The first Hell Knight's appearance was in Delta Labs 4. The portal to hell activates, and two Hell Knights emerge. They have noticeably more health than the regular Hell Knights fought later in the game, making them almost a boss encounter, reminiscent of the first bosses in the original Doom where the player must defeat a pair of Barons of Hell at the end of Knee-Deep in the Dead.

Near the end of Doom 3, before the player faces the Cyberdemon, turning left will bring the player to a brick with the id Software logo printed on it. Interracting with this brick opens up a secret room containing a PDA from id Software themselves. The PDA contains messages from the id Software staff, thanking the player for playing through to the end of the game.