Tbh I'm not such a FAN of the Artic Silver stuff at the moment. It works very well on some of my systems, but extremely poorly on others; it appears to be very very tempermental over what its put on. Too much is also bad. Its only there to fill any microscopic gaps, as it conducts better than air.
As Stellios says, airflow is important. The ATX standard is suck air in the front and pushing it out of the back. The upcoming BTX standard is pretty much the same, except 1 larger fan is placed in the case and it acts to suck in, blow over the CPU, Chipset, graphics card, and then out the rear. Apparently its much better.
There are, of course, some more radical ideas - my current case is an Artic Cooling T1 (butchered a bit to fit everything in as its very very exact on the ATX standard - unfortunately not many mobo manufacturers are). It sucks in the rear, through 2 fans at the top where the PSU would normally be, then flows over the CPU down infront of the drives and then out through the PSU which is at the bottom front. Its very cool, but if it dies I'm screwed. My short novel is just a point to say, follow the standards!