In most Dr Lunatic levels, brains are present and have to be picked up to finish the level. (if set in the Editor, the game will not allow the player to win without collecting a certain number of brains.) Two Cheats force collection of, or bypass the requirement of brains. The collection of Brains is tracked by the Brainometer found in the upper-right of the screen. When the player collects all the Brains in a level, Bouapha announces "I'm Kool Kat Bad!" When collected, Brains give 25 points to the player.
Also, in Sleepless Hollow, you must collect all 100 brains throughout the game to proceed to the final boss, the Headless Horseradish. Zombies (or Super Zombies) do not drop brains in this game. The whereabouts of these brains could be tricky, or really easy.