Which command can I use overwrite the boot loader?
Once upon a time, all you needed was to boot into Windows and run this on the commandline:
C:\> fdisk /mbr
But not anymore. You'll need to use the Windows Recovery Console (from a Windows boot/install CD). So you need to boot into the Recovery Console and run this:
> fixboot
Or this:
> fixmbr [device]
Use the MAP command to find the correct [device] parameter.
Win2000 Recover Console
On Vista? EasyBCD did it for me. Literally one click, was very impressed. For XP, somebody else'll have to chime in.