Basic cooling theory.
3 methods of heat transfer.
Conduction (solids in contact),
affected by contact area hence the thermal pads and thermal paste. The reason for a thin layer is because different materials conduct at different rates (leave a wooden spoon and a metal spoon in the same a hot liquid for the same amount of time) and thermal paste ironically does not conduct heat but it does fill in gaps pretty well. Silver is better than silicon but in this case I would be hard pressed to bring reasonable figures to prove the extra expense is worth it.
Convection (fluids or fluids in contact with solids and the important one here).
Moving fluid causes energy transfer to be quicker (page 143: http://books.google.co.uk/books?id=IlkrE8x...lurgy#PPA143,M1
) hence the fans. Blocking a port* stops the fluid flow and is what I see on laptops.
Faster fans (usually run off higher voltage sections of the board) make more fluid flow and so faster cooling. Small fans are usually more audible though so it is a tradeoff between sound and heat and as far as laptops are concerned space too.
Dust increases force required to move the blades and messes up airflow which is why we clean it out.
*reason 1 why you do not have it on your lap and I have also seen laptops sag and overheat because of it.
Radiation (only applicable in situations of very high temperature or if you are in a vacuum as it is then the only method of transfer).
Latent heat (simplified version)- temperature is an average of the kinetic energy of the atoms/molecules in a material. For a material all atoms/molecules need to reach a given energy for a substance to change physical state and this energy difference between the average reaching the point and all of them is known as the latent heat (usually of melting or of evaporation or their counterparts depending on what is happening.
Heat sink as the name implies holds heat energy and will usually provide a better way to transfer heat away (moving it to another area or via heat spreaders (remember surface area). Space is at a premium in laptops so they are not usually that good on any front).
This is the principle behind air con, fridges and wax based cooling/temperature change slowing (see phase change cooling). Wax based cooling and liquid nitrogen exist in computing, a further type just being made relies on the simplification that air speed as you near the device goes to 0 (hence the surface area stuff) and creates mini hurricanes/electrical charges to disturb this and so increase cooling (quite well I might add).
In computers silicon stops functioning a desirable manner at temperatures of around 100 degrees C but lower temperatures are enough to cause issues with the setup (see electromigration- this is the thing that shortens the life of your chip when you overheat it) so we try to keep temperatures down. Note new computers and the more expensive components will have good temperature sensors while the old/low end stuff will need to be taken with a pinch of salt either because they are not so good or because they are found in places further from the actual heat source. Modern computers have a cutoff point when it comes to heat (old ones would simply keep working until they didn't).