If your talking about the type of clocking that notebooks perform when heating up, that clocking is done by changing the multiplier, not the FSB. Most notebooks run a FSB that cannot be changed.
A high FSB can cause other components in the PC to fail, so it's important to have quality components. The majority of today's PC's allow for some sort of thermal protection for the cpu in the bios, so the cpu itself isn't what I'd personally be worried about. Be worried about your vid card and drives..
If you wish to overclock, then I'd do it continually, and use the bios' thermal protection. If it crashes, then you've got it set to high. After overclocking, you should tax the system anyway to find out where the temps are maxing out. When windows crashes due to overclocking, it shouldn't affect the protection afforded by the bios.