In our noise level tests we switched off all the case fans and replaced the AMD Radeon HD 7950 graphics card with a HD 5550 passive model so were just taking into account the noise generated by the cooler fans themselves.
We measured the noise level with a Digital Noise Level meter at a distance of 1 m from the front of the system.
With the fans spinning at maximum speed, the noise level was unbearable, however in PWM mode, the noise was reduced significantly.
Unless you're looking to achieve overclocking records the small sacrifice in terms of cooling ability is definitely worth the significantly lower noise level.