Doom II has two secret levels designed as a tribute to other id titles. The first secret level titled "Wolfenstein" is largely based on the first map in Wolfenstein 3D. A secret exit in the level leads to the second secret map, titled "Grosse", referencing Hans Grosse, the first boss in Wolfenstein 3D. To beat "Grosse", the player has to shoot four hanging Commander Keens and flip a switch. Commander Keen is the protagonist in multiple platformer games also developed by id.

Whilst the first Doom had a shareware demo of its first episode available, Doom II did not. According to John Carmack, this was because people mistakenly consider themselves to have beaten Doom when they had only beaten the shareware episode.

According to Bobby Prince, the Arch-vile is an evil healer, who blasts his way through demons, but then reanimates all of them. The Dual Personality gave him the idea of giving it an evil laugh.

The laugh itself is of a young girl saying "why" with the pitched shifted down, and mixed with other sound. This was done as the Arch-vile doesn't understand why anyone would want to kill him as he sees himself as only doing good for his fellow demon.

In the Doom II final level "Icon of Sin", the boss is supposed to be a giant demon head with a fragment missing from its forehead. It says, "To win the game, you must kill me, John Romero!", distorted and in reverse to sound like a demonic chant. One can use the "noclip" cheat to enter the boss and see Romero's severed head which is skewered on a post. John Romero is the creator of the Doom series. The staff didn't like Romero due to his egotistical personality. They decided to get him back by making him the final boss.