The CPU fan is more than likely the thing causing the vibration to occur.
I'd recommend very carefully opening your PC while its running on your boot up and simply touching your heat sink to feel if its vibrating if it is then id say there is a 90 % chance its the CPU fan.
Easiest way to test that is in the center of the CPU fan (not the blades!) put your finger on it and apply pressure until it slows to a stop then with the CPU fan stopped momentarily using your other free hand touch the heat sink again with the fan stopped to see if its vibrating. If it isn't and the fans stopped its the CPU fan.
What you can do to try and resolve the issue is first make sure the screws holding the fan in place are tight if not tighten them if even then the issue persists then I would say take all of the screws out and try just putting the top ones in and let the bottom stay lose (worked for me) all else fails replace the fan they are like 10 bucks.
Lastly before you go touching anything make sure to ground yourself by touching something metal so you don't create a static shock in the PC and lastly make sure the fan is free of any dust to much dust can make the fan become offset and have it spin awkwardly making it vibrate.
So do I need to replace the fans? What do I do so that I could conclude that its actually a fan problem – soul – 2010-05-15T07:13:18.923
Put your finger gently over the fan. Apply pressure lightly-progressively, stop the fan (even CPU fan can be stopped for a few sec, dont worry). Listen. If the noise is gone, buy a replacement and go for it. (Also, you can apply grease on older fans like old GPU fans where replacement is a no go.) (And hell yeah you can kick the PC also which is more fun but its a bit risky. >.>) – Apache – 2010-05-15T07:38:49.777
My PSU fan is like this. I just launch some power consumer (gpu tester, cpu burner) and after a few second its gone. :P Well. Chieftec PSU..what did I expect? ^^" – Apache – 2010-05-15T07:39:40.553