Sounds like the hard drive... I'd try muting all the audio to check that if you think its not. Other than that - just check what apps are running when it clicks...
Have you contacted Apple to see if its an issue that they're aware of?
I've not got any messengers running. I know what a HDD click sounds like and it's not that; the noise isn't mechanical. Hasn't happened for a while now, but i know it'll be back.
I've just now muted all sound to see what happens.
Any other ideas? Generally I'll be running Firefox, Entourage, Word, Parallels and the Dashboard in the background.
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