The background story:

According to John Romero, the Boss Brain was originally just a dummy yellow circle sprite. Towards the end of the development of Doom II, one of the other programmers sneaked in the Romero's Head sprite, presumably hoping that it would only be discovered by Romero after the game was released. Unfortunately for them, Romero stumbled across the sprite while writing the sound effects code that made the brain scream when you shot it.

Eager to get the last laugh, Romero got Bobby Prince to record him saying the now immortal line, To win the game you must kill me, John Romero, and added it in as the boss wakeup sound, phase-shifted and reversed.

Source: loonygames interview with John Romero: