A while ago my laptop completely failed, no shutdown, just immediate power-off, after overheating when playing Portal. The dedicated graphics chip (ATI Mobility Radeon HD 2600) tends to get too hot if the laptop is put on the wrong type of surface - and I do mean a hard flat surface here - it was a laptop tray table.
I'm sure in some cases there may be little difference when using a cooler. However, I got
http://www.ebuyer.com/product/61069 and have noticed that the temperature recorded by Core Temp has dropped by over 15C using the fans on their high setting (audible), and nearly 10C on low (very quiet). Even the extra height gained under the chassis with no fans on keeps the CPU 5C cooler than before!
The fans in the cooler do not match up to the location of the CPU fan intake, but nevertheless I find that it makes a huge difference to internal temperatures in the fact that the bottom of the laptop chassis, which used to be very hot to the touch, is now kept at around room temperature, if not below. This seems to efficiently take the heat out of the laptop even without passing a stream of cold air into the CPU fan intake.