As per my point of view
please understand the merit and demerit of moving home folder to other file system

NTFS is not suitable for an home partition, there are certain type of file system objects (character devices, named pipes, etc) which are required for certain services but are not supported on NTFS. ^source

It's not a good idea to have the whole of /home in a fat32 or NTFS partition because those two Windows filesystems don't support Linux permissions. Also, the /home folder has many hidden files and folders (these have a leading . i.e for hidden files) for configuration and I don't know what effect this would have in Vista, or whether Vista would interfere with these..

But what I do is to have a separate NTFS partition for data and set up symlinks from my /home in Linux and whatever the equivalent is in Windows (links? shortcuts? ). So - say I have a 'Music' folder in my NTFS data partition, then I create a symlink called 'Music' in my Linux home and a link called - yes, you've guessed it - 'Music' in Windows My Documents. (I'm using XP.) In fact I also multiboot several Linux distros, so I do the same in each. Whichever distro/OS I'm in I can access the same files from my home folder by double-clicking on the symlinks (which look like folders with bendy arrows in Linux)

If I am wrong correct me