How do I set the main icon for the default Java Help Viewer?

Use the following method of javax.help.plaf.HelpNavigatorUI

public void setIcon(javax.swing.Icon icon)
    Sets the icon for this HelpNavigator.

You can also traverse the parent heirarchy of JHelpNavigator till you find a instance of java.awt.Frame. Once you have it you can call -

public void setIconImage(Image image)
    Sets the image to displayed in the minimized icon for this frame.
    Not all platforms support the concept of minimizing a window.
Parameters:
    image - the icon image to be displayed. 
            If this parameter is null then the icon image is set 
            to the default image, which may vary with platform.