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bbfa235
(Get the code!)
I just tried to find a way to achieve this in Natty, and I can't... I have an on-board sound card connected to speakers, and a separate USB headset used for Skype/SIP and various other VoIP software like Mumble... You can change the input device for an application once it's running using Pulse Audio Volume Control, (but not sound preferences)... and you can change the default input and output device for the system in the gnome preferences... but not on a per application basis.
There really needs to be a way to do it in Empathy, and if I'm not understanding what is required to have Empathy open automatically when I log on, ring on the speaker, and have the VoIP call on the headset... then the UI needs to be improved.... but I'm fairly sure there is no way to do it.