The programmers added a picture of John Romero's head on a stage at the last level. John noticed that and added a sample to the last level of him saying: "To win this game you must beat me, John Romero". The sample was pitch-shifted and reversed.
There are two bonus levels which are recreations of the first and ninth levels of Wolfenstein 3D (the game which launched the "first person 3D shooter" genre).
The full list of songs whose melodies have been borrowed or copied either wholly or in part (Doom 2 only; alphabetical order by artist): Alice in Chains - "Angry Chair": Map25. Alice in Chains - "Them Bones": Map23. Black Sabbath - "After All (the Dead)": Map10. Pantera - "This Love": Map18. Slayer - "South of Heaven": Map07.
The only way to see John Romero's head on the last level is to invoke the cheat code that allows you to walk through walls ("idclip" on the PC version) and walk through the giant face.
In Doom the character's name is William "B.J" Blazkowicz, 3rd or Billy Blaze the 3rd for short. Only in Doom 3 was character's name changed to flynn. Commander Keen is William "B.J" Blazkowicz 2nd aka Billy Blaze (second generation). Wolfenstein's character is William "B.J" Blazkowicz (first generation)