I am going to go ahead and add my 2 cents in here as well
FDISK is a DOS utility that can still be used on winxp machines (running NTFS). I use DOS all the time for one simple purpose. Booting utilities. DOS boots fast, a heck of a lot faster than a win xp PE, and I can run imaging, HD utilities, netboot, etc from a DOS based boot CD.
Now, FIXBOOT in the command console (terminal, command line, wtfe they all practically mean the same thing) rewrites the boot sector with a new one, while FDISK /MBR just gets rid of it.
One example when i use FDISK /MBR a lot is when I load Linux on a laptop at work for testing purposes and then when done have to reimage it. Well, I like to load boot loaders (mainly GRUB) on them which are located in the boot sector of the HD. I can reimage a system all day long with Ghost and it will not boot back into windows even after running the windows image back on the laptop. This is because the imaging software does not overwrite the bootsector.
Now, if you had booted off a Ghost CD and then did a disk to disk copy, I believe then it does a full sector by sector copy from drive A to Drive B (this is to answer the posters question).
For the most part DOS is dead, it is not as secure nor as robust as NTFS. Plus DOS based file systems have limitations that other file systems do not.
I have to agree with Kenin on this one for the most part. However, you can still use FDISK on non supported file systems to delete filesystems and wipe the boot sector.