The architecture of the Systray changed in Ubuntu 11.10. Now it's the Notification Area. The majority of old, familiar application no longer appear in the tray, where you expect them to be; unless you fool it.
Some systray icons for QT-based programs such as Skype and VLC are automatically converted into indicators by sni-qt.
Wine, Java, scp-dbus-service and the Update-notifier are whitelisted by Ubuntu, but you can whitelist all applications.
Using Dconf-editor, navigate to desktop > unity > panel. To get the equivalent of the Systray in the Notification Area for all applications, change the default list to [‘all’]. Or you can add program names individually, in single-quotes, comma-separated by coma, e.g., 'Wine', 'Skype' etc.
To reset the list, the default value is shown in the Dconf-editor ['JavaEmbeddedFrame', 'Wine', 'scp-dbus-service', 'Update-notifier'] or click on “Set to default”
in dconf-editor. RC