Whiny computers are driving me nuts, so I've just started trying to achieve near silence for the first time. Components in the computer industry always seem to be out of step with each other, and such a case is annoying me right now. I looked around for people writing on this topic, but I didn't see anything specific.
I used the following, although the specific components are irrelevant, as they are pretty similar in design approach to most current mid to high end devices:
An Gigabyte EX58-UD3R motherboard
An i7 CPU
A Cooler Master Sileo 500 case and
A Thermalright U120 cooler
The best CPU cooling, whether for quietness or massive overclocking, seems to be achieved by a crossflow cooler, like I have used, in a case with a nice big fan right behind that cooler, to whisk the warm air away to the outside world.
Most high end motherboards are now laid out like the Gigabyte one I used. They have a heatpipe connecting the warm bits around the CPU (i.e. the VRM and northbridge, and sometimes the southbridge too), and heatsinks designed to cool those parts using the air flowing out from downdraught cooling of the CPU. With crossflow cooling there is practically no downdraught. The CPU is much cooler than with a downdraught cooler, but everything in the surrounding area on the motherboards goes up in temperature. Its not easy to divert some of the airflow into the required places, and adding a bunch of tower type heatpipe coolers in place of the ones the motherboard maker fits would be painful and costly. It isn't easy to find ones that will fit in the relevant spaces.
Cheap motherboards, with more elementary cooling around the CPU have less of a problem in this area. Surely the expensive heatpiped motherboards are the ones most likely to be used with a high end crossflow cooler. Things seem to be screwed up.