As an early developer of audio products I struggled with this problem for years. There are some expensive solutions. So here are some cheap ones:
(1) The majority of the noise is transmitted from a new fan fan is to the case. Proper use of silicone attachments removes this vibration. The majority of times this has more effect than anything else.
(2) Purchase the largest fan you can, then take a spare connector and connect the 5v input to the ground output. This lets you run the fan at 7V, which substantially reduces its noise.
Rubber grommets on disk drives are also very cheap, if you can find them, and also stop case vibration very effectively. It's often difficult to find them though, so it's worth checking the next time you buy a case that it has them. The Antec Sonata has them for example. I agree quietpc.com is a good resource.