While most of the levels exist highly ruined, the developers first built every level as if nobody had ever walked in them. Going through each level with special developer-only 'weapons', level designers would then dismantle the levels in order to create a highly damaged effect.
The game contains several references to the original Doom games. For example, one of the magazines lying about has a "surprised" face on it - that of the Doom Marine from the first two Doom games. Also, the "player face" on the arcade machine is that of the Doom Marine.
In the original Doom, the player lost all their equipment (except for a pistol and 50 bullets) at the beginning of every new episode (for a total of two times). Although no reason was given for this effective "restart" in every chapter, the concept was carried over into Doom 3, and the player loses all their equipment (twice), on the journey to and from Hell. There are also several other holdovers from the original doom, such as a boss fight that consisted of two Barons of Hell, toxic sludge, and more.
Originally was not intended to be made. John Carmack, unimpressed with the current plan for the company's next game, told his co-owners that unless Doom 3 was id software's next project, he would quit.
Originally, the Soul Cube was going to be split into four sections, forcing the player to defeat each section's "Guardian". Designers felt that this would make the Cube seem weak, and opted instead to keep the Cube whole. However, this concept is reused for the Artifact in Doom 3: Ressurection of Evil, where the player have to fight Guardians in order to gain new special powers.
In the last level, just before the final boss, there is an empty room with the "Id" Logo on the wall. If you click on it the near wall opens in a secret room and you can take the "Id Pda" with the "Thanks" of the Id Staff.
The Doom 3 engine, id Tech 4, began as an enhancement to id Tech 3. During development, it was initially just a complete rewrite of the engine's renderer, while still retaining other subsystems, such as file access, and memory management. The decision to switch from C to the C++ programming language necessitated a restructuring and rewrite of the rest of the engine; today, while id Tech 4 contains code from id Tech 3, much of it has been rewritten
In one of the mails found/discovered in the PDAs lying around the base, there's a "futuristic" version of an IP address. If you "subtract" a few digits from it so it becomes a "normal" present-day IP address and perform a "reverse DNS" you'll get: "idsoftware.com", the domain/site of the creators/developers of the game.
Originally the story of the Soul Cube was to be told to the player through hallucinations. These hallucinations would trigger during any type of portal transport to add both back story and tension. This was to show the player that the cube was trying to communicate with the player through the portals all the way from Hell. They would've been split into sections, and by the time of the final transport, the player would be aware that the Cube was trapped in Hell, split into sections. However, this back story would've hurt pacing too much, and many of the elements the cut-scenes would've shown were better delivered in other ways. Also, the element of the Cube being split was also removed.
Betruger wasn't originally intended to be the obvious villain as he appears in the game. Originally the player was supposed to assume that Swann was the villain and Betruger would emerge later as the antagonist. This was cut to streamline the story.
If you read Jack Smith's emails on his PDA, one of them makes reference to an accident happening to a worker nicknamed "TorsoBoy". This is a wink-wink reference to the ''Weird Al' Yankovic' song "Albequerque" which features the nickname TorsoBoy. In fact, in Doom 3, the machine in which the accident occurred around was called the "Albequerk Compactor".
There is still a similarities between Doom 3's engine with id Tech 3. You will notice the camera bobs when you crouch. Also the file management is still the same, though files are stored in different format
The name of the doctor responsible for the disaster is Dr. Malcolm Betruger. The German word "Betrüger" means "Cheater" in English. Id Software always tried to prevent cheating in the multiplayer mode of their games. So the bad-guy of Doom3 is a cheater and in reverse cheaters are bad-guys.
The trivia item below may give away important plot points.
If you kill Larry Kaczynski and take his PDA, you will find an email from a "John Okonkwo" that turns out to be the well known "Nigeria Scam", which is apparently still assaulting inboxes well into the 22nd Century.