Solution I came up with in the end (hacky I know) was to run Skype as a root process - it seems root processes attach to the user currently in operation, so it appears as a normal app to the "Skype" user but is never detached from making sounds.
Another solution would be to run the whole thing under Panther...
I had a quick look at Growl (only a quick one though) and couldn't find any easy way of letting it pop up messages for all users - they seemed to just appear on the "Skype" user screen. I might have another look.
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I can't understand why people are frightened of new ideas. I'm frightened of the old ones. -- John Cage (1912 - 1992)
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