Doom 3 explains why there are chainsaws on Mars: They got mixed up in an order for jackhammers.
Late in the third game, you can come across a terminal covered in blood. The terminal details how to perform a sacrifice to the forces of Hell written like cookbook instructions.
MAP20 of Doom II, Gotcha!, becomes this in retrospect- the demons deployed their two most powerful monsters in the same spot, thinking it a foolproof plan. If Doomguy plays his cards right, they'll end up... fighting each other.
The Xbox 360 Arcade port of Doom II has achievements that quote the Doom comic, including "You Have Huge Guts" for killing a Cyberdemon with your fists.
One visual glitch is that, regardless of where on the image an enemy's weapon is, its attack emerges from its midriff. This resulted in unintended humour in the "Ultimate Simpsons" Doom mod, where the Cyberdemon is Mr. Burns... and his rockets emerge from his crotch.