Here is something you might already know, but I for one didn't notice it until today (thanks to Georgi and Rolandixor!): Skype, VLC and other Qt applications have an indicator in Ubuntu 11.10 Oneiric Ocelot thanks to a package called "sni-qt" that converts (automatically) Qt systray icons into indicators.
(Both Skype and VLC icons are indicators - notice the border on the Skype icon, that's indicator-specific)
The converted Qt indicators look and behave the same as regular Ubuntu indicators. All we need now is monochrome icons (I'm not sure if that's possible for Skype).
The systray is still available for Wine, Java, scp-dbus-service and Update-notifier only but you can whitelist all applications just like in Ubuntu 11.04 - and that bug that caused the non-clickable indicators issue seems to have been fixed.