The goal of this particular system is to build a quiet PC that also performs well and won't break the bank. The goal is not to build a completely silent PC.
There are lots of tricks you can do, if you have the money and inclination to build a completely silent PC, but you'll almost always forego some level of performance. In addition, it will likely cost more. For example, Zalman makes the TNN 500F, a pricey (and heavy) case that can act as a giant heat sink.
What I wanted to focus on is a practical PC that offers good performance and is very quiet. One of the key factors is the cooling fans. Most cases ship with some form of exhaust fan; even fans that are supposed to be quiet, often are more noisy than they need to be..