I had some vibration/noise problems with my last system. I found that it was due to one of my fans causing my motherboard tray to vibrate. What you need to do is locate the source of the vibration in your case and find some way stop it.
For example, maybe a fan needs to be oiled, or something is not screwed down tight, or an unsecured part of the case is somehow vibrating. I remember I fixed a part of my case from vibrating by using a big glob of poster ticky-tack, you know, the stuff you use to stick posters to walls without having to use nails.
Hope this might help