Skype misbehaves a little by appearing as a system tray icon in what is now the notification area and it also displays all wrong by, for example, sometimes appearing as a small pixel and not the full icon. Adding to this the fact that the Unity launcher will load multiple instances of Skype rather than jump to an existing open session means that I for one wanted to remove Skype from the Ubuntu notification area.
To remove Skype from the tray or at least not have it show there this is one method.
1) install dconf-editor
2) run dconf-editor
3) navigate to: Desktop > Unity > Panel and highlight the panel option.
4) In the pane on the right you'll see a string of items which are allowed to display in the Notification Area as if it were a System Tray, Skype is one of them, so carefully remove it making sure you don't mess up the formatting of 'item','etc','etc'
Also to stop mounted devices showing in the Unity Launcher
Under Desktop > Unity Devices > Device Options > Never This does not allow mounted devices to appear in the Launcher.