I was thnking the same myself yesterday when I was stress-testing. Coretemp always reads a few degrees lower than TAT. I think I read somewhere that one measures the temps of the die, which will always be hotter. I could be wrong, though.
Speedfan gives me three readings, two "Core" readings, and a "CPU" reading, the CPU reading is always a couple degrees cooler than either of the cores, so I think they measure each core, and one outside the core, like in the IHS, or on the PCB side.
They aren't all measuring the exact same thing. As long as changes to your system (like getting a new CPU cooler) make about the same difference for all three readings, then you really shouldn't care all that much.
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