In 8.5.2, you can now control your audio conversations directly from the system tray, without opening the Call window. All you need to do is right-click the call icon, to see the options:
Left-click the icon, or right-click and choose "Call with <user>" to open the full call window.
When you mute the call, you see a "muted" icon in the system tray:
Sametime 8.5.2 Features: New system tray control for audio/video