If you can't live without an application that still uses the old notification area, here's how to get the Unity systray whitelist back in Ubuntu 13.04
sudo add-apt-repository ppa:timekiller/unity-systrayfix
sudo apt-get update
sudo apt-get upgrade
You install Skype and expect it to work as it used to. But if you close
the main window - you soon notice that Skype icon is not being displayed
in top panel.To fix this you will need to run a few commands. So open up your terminal and run this:
gsettings get com.canonical.Unity.Panel systray-whitelist
You should get something like this:
['JavaEmbeddedFrame', 'Wine', 'Update-notifier']
Basically this means, that Skype is not whitelisted, thus is not allowed by default to display
its tray icon. We need to fix this. Append 'Skype'
to the list so that you have something like this:
settings set com.canonical.Unity.Panel systray-whitelist "['JavaEmbeddedFrame', 'Wine', 'Update-notifier', 'Skype']"
Now just copy this to your Terminal and execute the command. Reboot afterwards. Now you should see the icon.