The first thing to remember is that there is 2 elements to quiet efficient PC cooling - CPU and case cooling. If either of these are noisy or inefficient, then you will end up with a noisy or hot PC, so both need to be tackling both elements in tandem.

CPU cooling is fairly basic nowadays as there are some good coolers out there - use a cooler processor (eg Athlon XPs are cooler than non-XPs), don't overclock to extremes, and choose a cooler that will accept a 80mm fan rather than 60mm as it allows slower/quieter fans to achieve the same airflow as a faster/louder fan. In the past 6 months, the Alpha PAL8045 has been really popular. The Silverado, and Zalman Flower are also well respected. I'm not sure about stuff thats come out in the past couple of months though. Stick a good quiet fan on it (papst, panaflow are respected for their noise levels.)

Case cooling is a trickier subject - without efficient case cooling, you cannot get good CPU temps. Period. But every case fan you add potentially adds noise as the fans are basically open to the atmosphere. So it's about striking a balance. The idea of using temp-controlled case fans is a very good one - when the CPU is idling, you should be able to get good enough temps using only 1 quiet case fan and a quiet PSU fan. But when you're playing RTCW 3 hours straight you probably will need another fan to kick in. Again, panaflow or papst fans are good quiet fans.

www.avsforum.com has an Home Theater PC forum which is a great resource for this kind of information.