I would be very wary of using hardware temperature monitoring. Most use a sort of diode to measure temperature which needs to be placed as close to the part as possible. For processors, this can be tricky, as placing it between the heatsink and the chip's heatspreader will break even contact with the heatsink and actually cause temperatures to rise. Placing it on the outside will give you an idea of the surrounding temperature, but count on the actual core temp being 10-15C higher. If there's a sudden cooling failure, your chip will shut off long before the bay solution picks it up.

When I was working for an OEM we discussed thermal issues with our Intel rep often. Starting with the Prescott core the intel motherboards and software would measure directly from the onboard thermal diode built into the chip. This is really as close as you can get, and we found it to be very reliable.

The other solution would be to use a thermal diode, but with some variations. To ensure we were still geting optimal contact with the CPU, we would carve a channel into the heat spreader deep enough for the diode to sit flush with the heat spreader. This would run from the edge of the chip to the core. We'd then epoxy the diode in place and hook it up to our monitor for thermal validation. This was a very tricky and dangerous process, as there was a very high risk of drilling too deep into the heat spreader and damaging the core.

I'm guessing this is a little overboard for your needs (and certainly mine!) but I would give a utility such as Intel's Active Monitor a try.

Hope this helps!