Canon

Canon would refer to the body of works related to a particular subject and considered proper history and continuity to series. The Doom series may contain more than one canon based on storylines of various reboot universes.

See also Timeline.

Background
In case of Doom there are very few official comments that relate to canon or discuss canon directly. Sometimes official positions are contradictory or changes over time (or retcons are made).

As such there are a number of fan theories as to what comprises canon or what is not canon these can only be considered Fanon as there is very little as far as confirmation on what is canon.

In addition the Doom series has received a number of spinoffs and reboots throughout its life as well as tie ins.

Each reboot could be considered separate canons or alternate universes as part of a multiverse (Quake Arena backstory for example, Arena Eternal outside time and space, with heroes from various "alternate universes").

Tom Hall and John Romero have confirmed that several ID series are in fact connected. Doom Marine (from Doom/Ultimate Doom) is a Blazkowicz descended from Commander Keen, and William J. Blazkowicz before himhttps://www.google.co.uk/amp/s/arstechnica.com/gaming/2018/01/id-software-co-founders-confirm-that-its-biggest-games-heroes-are-all-related/%3famp=1https://www.resetera.com/threads/keen-blazkowicz-and-doomguy-are-all-related-tom-hall-confirms.19853/ (this does not apply to the MachineGames reboot universe however which follows its own universe with an alternate history for B.J. and a different family tree, and its own alternate Keen family as part of the ID multiverse). This is also mentioned in Wolfenstein/Doom RPG series as well. See ID multiverse timeline.

In both Doom RPG website and Doom 3 boxset the hero for most of the games is alluded to be the same hero in Doom 1-3 (and the RPG series). However, the exact order of the series is not entirely clear. With some interpretations placing Doom 3 as a sequel after first two games, and others as a prequel. A number of sources would support the idea that original Doom series takes place almost a century before Doom 3.

However Doom II's marine may or may not be the same character or a separate character from the Doom I character depending on different manuals and websites. His backstory differs from that of the original Doom character in that he fought on UAC Mars Base and escaped in a drop ship (mirroring events of Doom 3). Whereas as original Doom character fought in Phobos and Mars and in both original Doom and Ultimate Doom reaches earth via transporter gateways. Both Doom RPG website and Doom 3 BFG Edition try to establish that its the same Marine in all the games (however this would ignore certain details from other manuals or the games themselves, or at least make things in the timeline far more convoluted, or at least in an unknown order). Doom 3 BFG Edition's manual also goes as far to include Lost Mission and Resurrection of Evil in that claim (which is unlikely considering that in-game clearly indicates they are seperate Marines with different ID numbers, and in case of Doom 3 and Lost Episodes occur concurrently with each other).

Quake Champions brings back Doom (Quake III Arena), now listed as Doom Slayer, and mentions his pet Daisy confirming a link between Doom 2016 and Doom 1. Doom Slayer also comes with his uniforms from Doom 2016 (Praetor Suit), Doom Classic (Doomguy), Quake Arena (Arena), and Doom 3 (Doom Marine), and biography details that links all the games together.

The game also brings new MachineGames William Blazkowicz from his "universe" to the Arena Eternal (the place outside of time and space).

The Fanon tends to argue against the veracity of some of these sources, assigning different levels of theorized canonicity to the various references. But for most part ID's internal position is not known.

Levels of Canon
Note: This is general opinion of the Fanon, not necessarily developers or Bethesda's positions on the matter.
 * Developer Commentary: Occasional discussions on what is canon in developers minds, but it is rarely touched upon. But some of this maybe ignored or superceded by later content, or rebooting of the series.
 * Games: These are generally considered to be primary canon, or may comprise more than one canon (Master Levels & Maximum Doom really has no story (or unused 'fanfic' backgrounds for when the levels were originally intended to be fan wads)).
 * Manuals: Generally considered canon, but may contain contradictory materials in later releases of the games (BFG Edition Manual for example). Not all the manuals agree with each other, sometimes being replaced with new manuals with alternate information in later releases of games.
 * Websites: These come and go, and are not often maintained and erased from the internet after a few years. Information is usually quite official, but only a few broken backups may remain.
 * Id Multiverse/Universe: This is comprised of crossover material and confirmed 'shared universe/multiverse' of other iD games. These are confirmed by current and former iD developers, and tied into some of the games such as Quake Arena, and Quake Champions.
 * Novels: These are generally considered canon. The Doom 3 novel in particular mirrors Doom 3. Certain details and characters from the two books have been incorporated and influenced material in other games such as Doom RPG (but not necessarily adapted directly). Flynn Taggart and his Taggart Comic Group are referenced in Doom Eternal but how that relates to overall canon is up for debate (see Doom Reboot timeline and Doom novels timeline, Player Customization and multiverse for some possible theories).
 * Movie/Novelization: This canonicity of this source is unknown. On one hand it takes place in an era largely not covered in other sources (Late 2020s-2050, see Film timeline somewhat similar to the Doom Timeline of the classic games), and thus could be seen as a prequel (to Doom 3, and taking place after original Doom series and Final Doom). On the other hand, its sort of a generic story, highly influenced by Doom 3's story. Almost a retelling without a proper demonic invasion (just humans mutating into monstrous creatures). But the novel might hint at very early invasions in ancient Mar's history. The sequel has an alternate Dr. Malcom Bertruger, and thus is less likely to fit with events of Doom 3.

Crossovers

 * Wolfenstein, Commander Keen, and Doom are connected according to Tom Hall.
 * Wolfenstein RPG and Doom RPGs include crossover material with a number of ID series and each other. Even as much as mentioning Orcs & Elves series.
 * Doom II RPG and Doom Resurrection have references to each other. The character Sam appears in Doom Resurrection until it is destroyed saving the player character's life, and its remains are rediscovered in Doom II RPG showing its final outcome. And the character Garrett is cross referenced in both. Both share the same sections of Hell named Gehenna and Abaddon.
 * There are some crossover material between Doom, Doom 3, Doom (2016) and Quake Arena III, Quake Champions. The latter also has crossover with MachineGames Wolfenstein universe. Quake Champions is said to be a prequel to Quake Arena which also has version of Doom Marine from another era.
 * Doom RPG and Doom 3 novels share details and backstory. Ian Kelliher, and the Doom RPG website claims that the hero is the same hero from Doom I, II, and Doom III. Deimos is already missing seemingly a nod to the original Doom.
 * The backstory in Doom II manual is similar to the plot of Doom 3, with lone space marine saving Mars Base. Doom RPG also has a similar plot. The only difference is when these times take 'chronologically' (Doom 2 is likely roughly 21st century, and Doom 3/RPG both take place in the 22nd).
 * The protagonist of the Doom 3 novels shares the same last name as the main character in Quake II (although there is no known direct connection between the two).
 * There are crossover elements in R.A.G.E. such as Mixom corporation. However the game is likely in a parallel universe where earth asteroid hit earth on August 23, 2029, and main character wakes up 108 years later in 2135 which is only a few years before Doom 3/4 which are each set roughly in 2145-2149. Based on what is known about earth in Doom series its unlikely its as bad off as it was in Rage 10-20 years before. On the one hand asteroid Deimos was left to crash into the earth in a few years... Assuming events of the novels 'happened' in one timeline as well...
 * Doom 2016 and Doom 3 are likely in alternate earth universes, although the same Marine apparently travelled through Worlds and Time to both according to Quake Champions, and info in Doom 2016. Alternatively Doom 4 might be set far in the future after a 'calendar change/year reset' (see Doom novels timeline).
 * A comic in Quake for Saturn included and adventure following Quake Marines Dank and Scud run into the Doom Marine during their adventures. Assuming that Quake took place between 2008 and 2108, he'd either have had to have time travelled, interdimensional traveled, or the date would have to be set closer to the original Doom Timeline in the early 2020s.
 * Although Doom 3 is said to be in same universe as Doom I and II (and Doom RPG) it is unknown if it is a prequel or a sequel in some fashion. Quake Champions is not clear, but just includes elements of the story in the back information for Doom Slayer, but does imply to be the Marine's first time on mars, and his first encounter with demons. The backstory for the Marine/Slayer is similar to manual prologue in Doom 1, however assuming that Doom took place in early 21st century (as per SNES and novels), then Doom 3 would have to occur in the far future (almost 120 years later) which would have problems with Doom 64 (unless Doom 64 was after Doom 3 and Doom RPG), but this would require for Doom Marine to have gone into stasis at some point on Earth most likely, before returning Mars. Doom 64 is implied in Doom 2016 and even more strongly in Quake Champions to be events that lead up to 2016 game.
 * Keel in Quake Champions appears to be based on Revenants.
 * The UAC is mentioned ins ome of Quake 4's background. According to Quake IV: The "Armstrong" was an Orbital Space Station in low orbit around the Earth. During the Strogg invasion of Earth, it was used by the U.A.C. to study and store creatures and weapons developed on Mars. When the Strogg invaded Earth, the station had been turned into an Orbital Defense Platform, but it was ultimately taken down by the Strogg. During this incident, Kane found an old U.A.C. weapon which he used to survive. He turned out to be the only survivor of this attack, but The United Nations kept him quiet about this incident, leading to rumors that the weapon wasn't all he had found. As Quake II/IV takes place in 21st century and thus likely overlaps the orignal Doom Timeline, and there are no direct references to Strogg invasions in any Doom related materials its possible that Quake II/IV universe is also in a seperate earth of the iD multiverse.
 * A level in a Wolfenstein 3D expansion has B.J. traveling to the future into a UAC base in an unknown location. In Spear of Destiny: Mission 3: Ultimate Challenge, Hitler has found a way via the occult to see into the future and even travel there, and he's stealing technology in order to give the Nazis and advantage over the Allies. At one point B.J. Blazcowicz is transported to the future into a UAC base where he sees UAC boxes, and Doom computer monitors showing the sun. Like in Doom its been invaded by a Demonic force (Devil Incarnate).
 * All the collectable dolls/action figures in Doom 2016 are based on other ID franchise and classic Doom games.
 * Rage has a secret teleporter leading to the first room of E1M1: Hangar. There, the player can pick up a Doom Marine Bobblehead. There are also similar secret areas calling back to Wolfenstein 3D and Quake.
 * The Soul Cube appears in Doom 3, Doom RPG, Doom (2016), and Doom Eternal.
 * Classic Doom games can be seen Doom Eternal/Doom 2016.
 * Super Turkey Puncher 3 can be found in Doom 3 and Doom 2016.
 * Sarcochagus holding a 'great Hero' (showing an image of Doom Marine) are found in Doom 3, Doom (2016),
 * Stroggs are referenced in Doom Eternal.
 * BFG10,000 (from Quake series) makes an appearance in Doom Eternal in a magazine.
 * The last level of The Lost Levels for Doom 64 quotes the Slayer's Testement, linking it to Doom (2016)/Doom Eternal. Doom Eternal has a flash back to Doom 2016.
 * Doom Eternal makes a number of references including to Daikatana, Half-Life, Doom Novels (Flynn Taggart), classi Doom games, etc.