HDHacker can be used, for example, to save and restore a particular boot manager (such as LILO, for example) before a new Windows setup (which, obviously, overwrites it). An MBR and BootSector backup can also be useful for simple precautionary purposes too, since sometimes viruses or other OS setup (like Linux) could overwrite and/or alter the MBR/Boot Sectors, making it impossible to start up previous OS and/or access datas stored on the disk. HDHacker can provide "insurance" against all these types of loss.
