I figured out tonight, that in my case the noise comes from the intake/exhaust fans. I can "lower" the noise / prolongate the "pulse" by setting the rpms at 800 for both fans (as stated in http://discussions.apple.com/thread.jspa?threadID=1971943&tstart=0). Now, because I've isolated the causing, I may ask for a replacement of the fans.
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Mac Pro ...ooOOOoo...oooOOooo... fan noise
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