Comment 8 for bug 596879

This whitelist implementation works very well for me, it gives flexibility to allow users to add items to the whitelist for apps that do not yet have indicator support and by default does not allow every single app to take over your systray.

@Dmitry: The whitelist is stored in dconf so you can modify the whitelist using gsettings:
gsettings set com.canonical.Unity.Panel systray-whitelist "[ 'JavaEmbeddedFrame', 'Wine', 'Skype', 'gajim' ]"