This question has been repeatedly asked in regards to Intel Core 2 Duo E6x00 series processors.
Applications like Speedfan and Everest Home Edition will read temperatures from the motherboard die socket sensor. Depending on thermal conditions this temperature will be up to 15-20C lower than that of the actual processor "core" die.
The Intel Thermal Analysis Tool reads temperatures directly from the Core 0 and Core 1 die's.
These temperature's will be higher than that of the motherboard socket sensors. However they will be in the same thermal range as the Integrated Heat Spreader (IHS) of the processor.
The accuracy of TAT is far greater than that of SpeedFan as the thermal detection sensory algorithm is far more sophisticated and in depth, and is less affected by analogue > digital conversion errors.
The Intel Thermal Analysis Tool itself is designed for use with Intel motherboards. However it will work perfectly with almost all boards using i975 and i965 chipsets for Core 2 Duo processors.
If you own a motherboard which contains an i975 or i965 chipset TAT will work perfectly and will display very accurate Thermal readings of your processor(s).
Intel specify maximum Thermal Temperature's for the IHS.
However under logic, given that large amounts of thermal energy in the form of heat are displaced from the transistors, it is sensible to assume that the temperature of the core and the IHS are infact very similar.
Therefore you should assume TAT to theoretically also display IHS temperature levels (up to 10% error Core > ISH).
Therefore use TAT to check if your processor(s) thermal levels are within the rated 60.1C.