My new tower came with a insanely loud whirring fan noise.  After five phone calls to Apple, I convinced them that the sound was real and that it wasn't going away.  The only thing I could do was keep putting it to sleep to shut the sound down, but on waking up, the sound would be back in a few minutes.  The exact day I received the FedEx labels from Apple to send it back, the sound stopped.   It's been quiet so far (knock on wood!).  It's as if the poor thing knew it was about to be sent back to the lab to be dismantled and tested.  I'm glad it decided to stay ;)