The 7200 RPM drives are known for having loud noises when installed in laptops. That is, as I understand it, the reason apple does not install them from the factory.
If the OS is pausing and you're hearing clicking, I would assume that there is a problem with the HD. Some HD's are just loud though. Best way to test it would be to mount another HD inside and clone (http://www.bombich.com/index.html) your system to see if the sounds and pausing OS problem continues.