Lots of panel apps do not work with new natty ApplicationIndicators based panel, but you can manually whitelist them to work with the old system or just use them all 🙂

gsettings set com.canonical.Unity.Panel systray-whitelist "['all']"

After that restart/relogin they should show up.

in case you want to revert it, the default is “[‘JavaEmbeddedFrame’, ‘Mumble’, ‘Wine’, ‘Skype’, ‘hp-systray’, ‘scp-dbus-service’]”