You can hide the VNC Server system tray icon whilst there are no connections active, by enabling the "DisableTrayIcon" parameter in VNC Server, Expert Settings. "0" means that the system tray icon will always be displayed, which is the default setting, so set it to "1" to hide the tray icon when VNC Viewers are not connected.
You can not hide the VNC Server system tray icon whilst there are active connections to the VNC Server for security reasons. If you have a legitimate need of this setting, please contact our sales team regarding an OEM license. They can provide a special license key that will allow you to disable the tray icon even when there are active connections. You can request this special license by going to:
http://www.realvnc.com/howtobuy/sales-team.html
Click on the "online purchasing process" link, complete the process as far as the "How would you like to purchase" stage, then "Enquire", enter the required details and a description of your request (Special license for disabling the tray icon even when there are active connections). Then "Submit enquiry".
Once in possession of the license, apply it to the standard VNC download and then go to:
VNC Server > More > Options > Expert tab > DisableTrayIcon
and set the value to 2 to disable the tray icon even when there are active connections.