you could end up with some dodgy problems in the end...
eg. drive letter problems because of the \DosDevices\* entries in HKLM\SYSTEM\MountedDevices\ (that is, if you repartition your hdd) and missing user settings (Local Settings, Application Data, HKCU registry, etc.) unless you copy the Documents and Settings folder too, but that would make the format even more pointless.
If you really wanted to do anything like that, you've chosen the wrong OS
Windows is just way too cluttered and messy by design to let stuff like that work without any problems.
/ 
