I think the workaround for the problem is to install laptop-mode-tools and in 
/etc/laptop-mode/laptop-mode.conf change line:
BATT_HD_POWERMGMT=1
to
BATT_HD_POWERMGMT=254
This of course sets default disk APM to 254, but with laptop mode tools my WD 
Scorpio Blue 500GB stays  pretty cool (about 43 degrees Celsius) and there is 
no idle drive "clicking" from now on. I've tested it on 11.04 and 10.04.
Maybe laptop-mode-tools should be installed by default on all laptops?

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https://bugs.launchpad.net/bugs/59695

Title:
  High frequency of load/unload cycles on some hard disks may shorten
  lifetime

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