To change the backgound color, choose -> and select the appropriate color in the palette, or choose a custom color.
The background color can also be selected from the command line: gchem3d --bgcolor=white or gchem3d -b white will open GChem3d with a white background in windows. Recognized strings are black (the default), white, and #rrggbb where r, g, and b are hexadecimal digits.