If you cannot boot into normal or safe mode, you will need to boot to the Windows CD. That may require that you adjust the boot order in the BIOS
/startup settings (to boot to the CD/DVD drive before the HDD
At the first screen, you can choose to run the Recovery Console, it will leave you at a command prompt, you can try entering
chkdsk C: /r
it may take a few hours to run.
There are not many other options that I know of. The next step would be to boot the Win CD and after you agree to the Eula, there is an option to repair the Windows installation, run that.