To me the most important thing about any software temp readings is calibration for your own use.
During my oc'ing, I try to find out at what temps orthos or 4 x P95 start to error, and also where a test folding WU will error. The max stable folding temp is what is important to me since my folding rigs run 724. This is usually cpu temps, but in the summer time, high mobo temps (~ 40c or more?) can also cause instablity.
I need to leave a margin of error to allow for build up of dust, changes in ambient temps so that I really only need to adjust things as the seasons change a bit.
So I don't consider any of the reported temps as absolutes, but rather a guage as to how close i am to instability.
I usually build more than 1 of the same cpu/mobo. I get a feel for consistency from one to the other and it makes oc'ing and diagnosis easier. I have multiple ds3's, p5b-d's, p5w64's, p5wd2-X's atm.
For me, core temp is pretty consistant across mobo's and c2d/c2q's, and i like it cuz of its small screen footprint.
For other mobo readings i like asus probe but i ignore cpu temp. Gigabyte easytune cannot be customized to fit well on a screen without obscuring other folding windows i like to monitor, as most of the folding rigs run 1024/768 or 1280/1024 res. All my ds3's are running linux atm so I only have gkrellm and lm-sensors to monitor with, but all my oc'ing is done in wxp.