An increasingly critical aspect of machine design is handling the waste heat and acoustic noise of operation. This may seem like a boring subject, but cooling is a centrally important one if you want your machine to last — because thermal stress from the electronics' own waste heat is almost certainly what will kill it. You want that fatal moment to happen later rather than sooner. On the other hand, cooling makes acoustic noise, which human beings don't tolerate well.
This tradeoff bites harder than you think; it's the fundamental reason that, despite my money-is-no-object premise in the Ultimate Linux Box artcles, I didn't go to relatively exotic technologies like liquid-cooled overclocking or RAID disk arrays for a performance boost. Sure, they may initially look attractive — but overclocked chips and banks of disk drives require massive cooling with lots of moving parts, and it's not good to be trying to do creative work like programming with anything that sounds quite so much like an idling jet engine sitting beside one's desk.
In 2001 we had already reached the point at which the thermal load vs. cooling-noise tradeoff is the effective limiting factor in the performance of personal machines. Ten years ago, even low-end and medium "server" machines differed from personal-PC designs in fairly important ways (different processor and bus types, different speed ranges, etc.) Nowadays specialized server architectures are in retreat at the high end of the market and everything else looks like a PC. And the difference between a "PC" and a "server" is mainly that servers live in server rooms, and are allowed to have monster cases with lots of noisy fans.
So how do we manage this tradeoff for a personal, desktop or desk-side machine? Careful choice of components and being willing to pay some price premium for cool-running and low-noise characteristics can help a lot. Even exceptionally clueful system integrators can't generally afford to do this, because they're under constant competitive pressure to cut price and costs by using generic components.
Reducing expected noise and heat in a design call for different strategies. It's relatively easy to find decibel figures for the noisemaking parts in a PC design. And, once you know a little basic audiometry and a few basic rules of thumb, it's not hard to form a fair estimate of your design's noisiness. Estimating a design's heat dissipation is harder, partly because the waste-heat emission of a PC's subsystems tends to vary in a more complex way than the acoustic emissions of the mechanical parts. This means that you can and should try to design ahead for low noise, but on the other hand expect to have to monitor for heat-dissipation problems in your prototype and solve them by building in more cooling.
Here's the basic audiometry you need to know to control your design's noise emissions:
Sound is measured in decibels, abbreviated dB, relative to the threshold of audibility, "A". (Thus, sound levels above that threshold are written "dBA".) The scale is logarithmic, with every 3dB increment roughly doubling sound intensity.
For sounds that are not phase-related, decibel levels add as a logarithmic sum. Thus if X and Y are uncorrelated sound sources,
dBA(X + Y) = 10 * log(10 ^ (dBA(X)/10) + 10 ^ (dBA(Y)/10))
A consequence of the above formula is that dBA(X + Y) cannot be more than 3dB above the greater of dBA(X) and dBA(Y) for uncorrelated sources (6dB for perfectly correlated ones).
Sound from a point source decays by an inverse-square law, roughly 6dB for each doubling of distance.
Important thresholds on the decibel scale:
Threshold of hearing
Rustling leaves, quiet living room
Threshold of distraction, according to EPA
Quiet street, average office noise
Normal conversation (1 foot distance)
Loud singing (3 feet)
Typical home-stereo listening level
The acoustic noise emitted by PCs is normally a combination of white noise produced by airflow, high-frequency noise produced by bearing friction in drive spindles and fans, and the constant frequency "blade passing" noise that all propellers emit (the latter is often more intense than white noise and bearing whine).
The best low-noise ball-bearing case fans emit around 20dBA. Typical sleeve-bearing fans emit 30-50dBA.
According to the indispensable Tom's Hardware site, you can expect to cut at least 5dB off the interior noise level of the computer with a good choice of case. We'll improve on that by adding sound-absorbing material to the interior.