Some I've heard of from Doom 3
-the hidden id room in the last level of the regular campaign. Pressing a hidden switch with the id logo will open a secret room with a PDA with various thank you messages
-the hidden Rage room in the last level of the Lost Mission campaign. Pressing the hidden logo will open a small room with some supplies
-when trying to use console commands to enter a cheat from Doom 1 or 2, the computer will say something like 'good memory'
-if you score 25000 points in the Super Turkey Puncher arcade game, you'll get an email talking about how your parents must be proud for raising a shining example of humanity and, as a result of spending so much time punching turkeys, your leave has been reduced by 2 weeks
In Doom 1, there's a Nine Inch Nails logo hidden in the first level of the fourth episode. Hitting a certain switch will lower a pillar revealing the logo. It's more apparent when viewing the area with the automap.
In the final level of Doom 2, the final boss appears to be a giant face on the wall with an exposed 'brain'. However, if you use the noclip cheat you can walk through the wall to find a human head on a stick, that head being the head of John Romero, one of the game's main developers. Furthermore, when you enter the level, you hear a voice saying some gibberish. When played backward, it says something like 'I am John Romero, you must kill me to win'. This is in fact the case, as you must shoot rockets through the 'brain' (really just a textured wall things can pass through) to hit the aforementioned head.
Been playing Doom a lot recently; can you tell? I got all 3 on the BFG Editon of Doom 3.