The Bin 3x3 command decreases the size of an image by a factor of three in each dimension. It does this by subdividing the original image into three-by-three blocks of pixels and computing the average of each block of nine pixels; the average becomes a single pixel in the new image.
This operation corresponds to three-by-three binning in a CCD camera, except that a camera integrates (adds) the charge from each contributing pixel instead of averaging it. To achieve this result, use Pixel Math afterwards to scale the image up by a factor of nine.
If each image dimension is not an exact multiple of three, the last one or two rows and/or columns of the input image are ignored.