> When the trigger on the Zapper is pressed, the game causes the entire screen to become black for one frame. Then, on the next frame, the target area is drawn in all white as the rest of the screen remains black. The Zapper detects this change from low light to bright light, as well as the duration of the "flash", as the different targets on screen (if multiple targets are on screen) will flash for different durations. This is how the game knows which target has been hit. After all target areas have been illuminated, the game returns to drawing graphics as usual. The whole process is almost imperceptible to the human eye, although one can notice a slight "flashing" of the image. Although the Zapper just detects light, it can only be used on CRT displays. It will not work on LCDs, plasma displays or other flat panel displays due to display lag. This darkness/brightness sequence prevents the possible issue caused by pointing the Zapper right next to or into a light bulb. Some people believe that this way it is possible to cheat and get a perfect hit score, probably misled by other older light guns which didn't use this method.
Alternative source: http://en.wikipedia.org/wiki/NES_Zapper#Technical_details
> When the trigger on the Zapper is pressed, the game causes the entire screen to become black for one frame. Then, on the next frame, the target area is drawn in all white as the rest of the screen remains black. The Zapper detects this change from low light to bright light, as well as the duration of the "flash", as the different targets on screen (if multiple targets are on screen) will flash for different durations. This is how the game knows which target has been hit. After all target areas have been illuminated, the game returns to drawing graphics as usual. The whole process is almost imperceptible to the human eye, although one can notice a slight "flashing" of the image. Although the Zapper just detects light, it can only be used on CRT displays. It will not work on LCDs, plasma displays or other flat panel displays due to display lag. This darkness/brightness sequence prevents the possible issue caused by pointing the Zapper right next to or into a light bulb. Some people believe that this way it is possible to cheat and get a perfect hit score, probably misled by other older light guns which didn't use this method.