most of the noise in a system comes from the fans. replacing he system fans with quiet ones is the first step. Sound dampening material will help some, but a noisy fan will still be a noisy fan. If you can hear the vibration of a hard drive then the rubber grommets for the the Hard drive mounts might be in order. The same goes for vibration from the fans and using rubber fasteners.
The fan noise from a GPU or CPU that is being stressed will be reduced by sound dampening material, but at the same time the added material will reduce the case's effectiveness to cool causing the GPU fan's to ramp up sooner.