Using an old trick to get it working in Natty, I had some success.
First I queried (get command) the current whitelist for old-style
notifications, and then copied it and added Skype to it (set command).
After reboot Skype appeared when loaded.

gsettings get com.canonical.Unity.Panel systray-whitelist

gsettings set com.canonical.Unity.Panel systray-whitelist
"['JavaEmbeddedFrame', 'Wine', 'scp-dbus-service', 'Skype']"

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https://bugs.launchpad.net/bugs/845173

Title:
  Missing system tray icon

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