In the hospital levels of "No Mercy", you can find a lot of X-rays with only four fingers. This is a reference to the game's cover art.

If you are an Infected when the elevator in "No Mercy" is activated and moving down, the number of what floor it is on will not change from "04", which is a reference to the "4" in the game's title.

In the hospital starting safe room of "No Mercy", there is graffiti on the wall reading "I killed..." and then lists different variables, including 53,594. This is the number of Infected you must kill to receive the "Zombie Genocide" achievement.