Windows Vista has a feature called BitLocker that allows for something almost exactly like what you're describing....
A cryptographic key, without which the system will not boot, can be placed on a USB drive and used to boot the computer. Without it, the computer is neither bootable nor readable by any third party, as it's wholly encrypted.
If you're considering a move to Vista, this is a handy (since it's built in) way to do exactly what you're describing.
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