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"The only thing I would do differently is get a quiet PC case."
A good case has to have good air flow and ventilation, and that means that some noise unavoidably comes out of the box too. However, if the case has a good ventilation, then you can have quiet fans, which really makes the difference in noise reduction. If the fan noise level is ok, getting quiet CD drives & harddisks is essential. After that some tricks with the case like putting noise damper material inside it etc. might bring some (probably marginal) extra noise level reduction too.
The truth is that a home made PC build from standard (non-quiet) components is likely to be a relatively noisy machine nowdays - also when compared to the Dell and other such PC's (Dell and many other PC manufactures have started to pay real attention to the noise issue recently.).
If you want to build a fast modern PC from components, I recommend to pay attention to the noise issue from the start, when choosing its components etc. Unless you want to develop a chronic headache and a disgust for computing because of the constant background noise...