Doom (series)/WMG

The Doomguy is Duke Nukem.
Think about it.

Doom 4 Will have you kill Satan while working with the main characters of Doom/Doom 2, Doom 3, and Doom 3: Resurrection of Evil.
Exactly What It Says on the Tin

The Doom Guy is Gordon Freeman
They both never talk, both have power armor, and both are a One-Man Army. Gordon was called into the UAC for his experience at fighting otherworldly beings in science facilities.
 * Gordon Freeman runs at an average human speed, and he can jump. Doomguy tears around at a superhuman 88mph, and can't jump at all. Gordon crumples when hit by explosives. Doomguy merely looks surprised. They ain't the same dude, dude.
 * He may be a lot older by the time period that DOOM happens, and counting more on his suit than before.
 * The Doom Marine(Stan Blazkowicz) doesn't even wear power armor, he wears titanium body armor that reveals his rock-hard abs. Besides Gordon's and Stan's faces and physiques are quite different

No, the Doom Guy is a demon.
And then Doomguy was a zombie.
 * No, hold on. Someone take this seriously for a second. Doomguy has been posessed, or transformed, or altered by Hell, but he's just so Badass that he hasn't even noticed. And if he had noticed, it wouldn't stop him.
 * Wait, isn't that in the Doom movie? Perhaps they got something right there?

I.M. Meen is behind the invasion of hell, and Scott (the boy from I.M. Meen) is the Doomguy
Note: This has spoilers from Wolfenstein RPG

After Scott escaped I.M. Meen's labyrinth, I.M. Meen swore that he would be back. Eventually, he died and went to Hell, where, with the Harbinger of Doom, they planned revenge on Scott, who is The Harbinger of Doom's powers helped all of I.M. Meen's monsters Take a Level In Badass, thus transforming them all into the Doom monsters we know (Troll=Demon, Spider=Arachnotron, Grim Reaper guy=Revenant, Guardian=Baron of Hell, Red ghost thing=Cacodemon, etc.), and so that they didn't go down in a few punches from a little kid. Scott happened to get a job on Phobos, and I.M. Meen saw it as a perfect time to unleash his new hellish army, which proceeded to zombify all the humans. Unfortunately for him, Scott also Took a Level In Badass and was easily able to defeat the demons, thus foiling I.M. Meen... or so he thought. His anger had turned him into the Icon of Sin, and the demons invaded Earth. Eventually, Scott defeated I.M. Meen for the last time, bringing peace to Earth. Although it does make me wonder what happened to Katie (the girl).
 * perhaps Katie is the second person on the cover!
 * Wait, Scott is Commander Keen?
 * OP: I thought it was implied that the Doomguy was Bj's grandson.
 * Billy Blaze (a.k.a. Commander Keen) is BJ's grandson. BJ's son Arthur changed his last name from Blazkowicz to Blaze in order to get a job as a TV show host.

Doom Guy is the grandson of Commander Keen
The Blaze/Blazkowicz family moved to Mars after the Vorticons were eliminated. During the UAC teleporter incident, old man Billy Blaze was taken prisoner by the Demon invaders. When the Doom Guy finds his grandfather being tortured by the Cyberdemon incarnation of Hans Grosse, he does the only thing in his power: he delivers a coup de grâce. The spirit of Billy Blaze rewards his grandson by returning him to Earth.

The abstract level designs aren't abstract at all
After the release of Doom 2, video game levels became drastically more realist, especially their layouts. After playing a game like Half Life 2 or more recent shooters like Uncharted it can be jarring to go back to games like Doom where the levels are more abstract and aren't made to resemble anything 'real'. Switches can reveal massive underground rooms or pits of toxic waste in surreal locations. These levels, though, are they really so abstract? Or is this merely a reflection of how the invading demons bring Hell with them? The levels get more abstract towards the ends of Doom 1 and 2, when the player gets closer to (or actually enters) hell itself, so obviously this abstraction is just part of how hell works.
 * If I remember, Word of God more or less confirms that, that the invasion of Hell itself actually affected the layout of the place. Take the first level, the Hanger. Aside from the handful of secret rooms/switches and the toxic waste leaks (which might've a result to damage to whatever was storing it), it looks somewhat normal. Later levels get increasingly strange, beyond the point where things like structural damage or such could explain the changes. Most likely, all the wierdness of the layouts were a direct or indirect result of the hellish invasion. Which goes nicely with the below guess...

All those secret stores of weapons and ammo were the result of the invasion.
As has been noted, the invasion had some effect on the layout of the levels. One might wonder why bothered to stash all those handy weapons and other items all over the place, while none of the actual demons can make use of them. It's possible they were intentionally hiding them, to simply prevent the enemy from making use of it all against. This might all explain why all those other space marines were wiped out, while the main character could manage despite being along and armed with only a pistol. In addition to being too tough for hell to contain, he was the only one with the wits or insight to figure out where all those goodies were hidden, while his comrades could only make do with the firepower they had available to them or could retrieve directly from the enemy.
 * Which doesn't explain why if the demons were smart enough to hide the munitions, they didn't simply destroy them outright or (in the case of weapons) damage them beyond repair. A few fireballs from a safe distance would have gotten rid of most of the ammunition, and either heating and twisting the metal or simply smashing it would have gotten rid of the guns.
 * Well, the zombie enemies were able to use some of the weapons, those possibly being whatever they were equipped with before they died. Maybe the demons were saving all that gear in case they felt the need to increase the firepower of their new undead minions? Though that would bring up the question of why they didn't go all out and make use of those weapons in the first place. Though if they did, we'd have to deal with BFG Zombies.

Doom takes place in the Warhammer40000 universe.
C'mon, it's got demons on Mars!

All of the demons are real people; everything is a hallucination of the character's mind.
Mars is also a hallucination as well.
 * Then we'd better hope he doesn't snap out of it... that court martial is going to be a BITCH.

The Martians in Doom 3 fled to Earth

 * And Doomguy is one of the Hero's descendents. This will explain how Doomguy is so Badass. He is a descendent of the Martian Badass.

Event Horizon and Doom are in the same universe
"You tunnelled though hell, you seriously didn't think there'd be a price?"

Doom 3 is actually a sequel to Doom and Doom 2

 * An interesting theory that this troper's friend made. Basically, humans on Earth eventually managed to get to Mars and its moons. However, the teleporter accidentally breached Hell, causing an invasion of Mars, its moons, and eventually Earth. The humans had enough technology to make Doomguy a Badass, allowing him to defeat the demons (Therefore, the original Doomguy is "the Hero"). This is the events of the original Doom and Doom 2. However, the humans were so devastated by the war with Hell that they were pushed back several centuries. Doom 3 takes place After the End where the descendents eventually go back to Mars, but since they weren't there at the first invasion, they didn't know why they shouldn't recreate the teleporter experiments, and History Repeats. These are the events of Doom 3.
 * The only thing this troper found that his friend didn't take into account was the Soul Cube (Though, judging by the Shout-Out to the original Doom cover on one of the tablets showing the Soul Cube instead of a machinegun, it could just be a Retcon).

DOOM 3 is not a remake or a sequel. DOOM 1 and DOOM 3 are the same invasion fought in different parallel universes
The demons are waging a multi-dimensional war. An infinite number of space marines - sole survivors of their respective parallel universes - are making their way into Hell to fight a multi-dimensional Eldritch Abomination.

The Cacodemon and Pain Elemental are related to one another in some manner, as well as to Unreal's Gasbag
I mean, they're both floating heads with gigantic mouths that can create things and launch them offensively (fireballs and Lost Souls). Eventually the two species, now inseparable, end up on Na Pali, becoming known as Gasbags - floating heads with a big mouth that can shoot fireballs (like the Cacodemon), but with usable arms at their sides and brown skin (like the Pain Elemental). Furthermore, the largest of these creatures can create smaller ones to help it in battle.

The Doomguy from the Doom comic is Deadpool.
He's Ax Crazy, conversant with weapons and seemingly can have a conversation with his dialogue boxes. Who else could he be?