Manual Mode
In Manual mode, the aperture and shutter speed values are fixed by the user. ISO Auto will change the ISO when the light levels change.
*When using the ISO Auto function in manual exposure mode the electronic analog exposure display of the camera will continue to indicate correct shutter speed and aperture settings when light levels change within a four-stop range. The ISO Auto system increases or decreases the ISO value to maintain the correct shutter speed and aperture value the user has chosen.
Shutter Priority
In Shutter Priority mode the shutter speed is set by the user and the aperture is determined by the camera system. If light levels change, the aperture will change as determined by the camera system. When the aperture determined to achieve the correct exposure is beyond the aperture range of the lens used, then ISO Auto will increase the sensitivity value.
Aperture Priority
In Aperture Priority, the aperture value is set by the user and the shutter speed value is determined by the camera system. If light levels change and the shutter speed required to achieve the correct exposure is beyond the shutter speed range of the camera, ISO Auto will increase the sensitivity.
*As the shutter speed range of a D-SLR is very large, it is rare that a shutter speed beyond the range of the camera (i.e. 30 sec) will occur under normal lighting conditions.
Program
In Program, Auto or any of the Digital Vari-Program modes the aperture and shutter speed values are determined by the camera system. As light levels change, the camera will alter shutter speed and aperture values to ensure the correct exposure. When the shutter speed required to achieve the correct exposure is beyond the shutter speed range of the camera and the aperture cannot be adjusted any further by the camera system, ISO Auto will increase the sensitivity.
Taken from the Nikon Website