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When looking for a good/max "Temperature." should I be looking at max "CPU" temp or max "CPU Heatsink" temp. Usually the heatsink temp is lower. My computer (Macbook Pro 6,2) measures both.

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You should look at CPU temperature.

Datasheets for processors usually show so called Tjunction which is the maximum temperature of the silicon chip inside the processor. The temperature which is displayed by processor's internal sensors is usually a tiny bit lower. After that you have temperature on the surface of the processor and temperature on the heatsink and so on. These temperatures are different because of thermal resistance. Thermal resistance impedes heat transfer and causes lower temperatures at the surface of the processor and heatsink and so on. These other temperatures which are sometimes displayed by computers are usually there to make it easier to detect problems with cooling system. For example if you have high CPU temperature and low heatsink temperature, that means that the contact between CPU and heatsink is bad.

Here's a nice video which describes how thermal design is done for electronic components. It's pretty much same for computers too.

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You should note both. Intel does specify maximum core temperature (Tjunction) but doesn't specify max heatsink temperature (Tcase).

On the other hand you need to compare them to see if the thermal paste isn't aging, if the difference is big then it may have dried.

You have to remember though that all thermal sensors are not calibrated well and can report values as far as 10 degrees from the "real" value.

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A note on the calibrated part. There are no actual temperature sensors in common processors. Instead they have overtemperature sensors. The point is that while sensor may show bad readings for low temperatures, its accuracy will increase as it approaches Tj, so computer will be able to act on time in case of overheating. –  AndrejaKo Jan 11 '11 at 3:56
    
This is actually incorrect. There are temperature sensors in current processors. Current processors provide access via a 1-wire or 2-wire interface. Older generation processors have a thermal diode which can be read by a remote temperature sensor. This is on top of the overtemp signals (of which there are two -- an approaching max threshold and have exceeded max threshold). –  hanleyp Jan 29 '11 at 16:00
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