I just upgraded to Ubuntu 11.04 - the Natty Narwhal and some new things need fixing.
One fix was to get back my Skype icon. The Skype icon was missing from my Notification Area and I was unable to sign out or to use Skype at all after minimising it.
This is a simple fix.
When you start Skype go to "Options">"General" and select "Start Skype minimized in the system tray".
This fixed the problem for me. Even if I restart the icon is still there.
