Using a folder on an ntfs partition as /home

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.

I'm currently storing the sub-folders of my home (e.g. ~/Documents, ~/Music) on an NTFS filesystem and it appears to be working fine a few months in.

As an example, here's how to host your ~/Documents in your Windows profile folders on an NTFS partition:

1. First make sure you have the NTFS partition set to automount so it's accessible to the system each boot.
2. Move any files that might have accumulated in ~/Documents over to the NTFS partition (e.g. mv ~/Documents/* /mnt/winblows/Users/Username/Documents/).
3. Now delete the ~/Documents directory and create a link to that NTFS folder in its place named Documents (e.g. ln -s mnt/winblows/Users/Username/Documents Documents).

Note: You might have to make ensure your ~/.config/user-dirs.dirs is in sync with the folder locations you've chosen (I did). See this answer for more details. Also, be careful to note the actual locations of your Windows user profile directories as these vary from version to version.

You would be better off not doing this if you want to ensure security. In older GDM versions (like what you would have found in 9.04) there was an easy option to ignore file permissions etc. However, GDM's (gui) options have changed a lot since then, and my suggestion is that you should avoid the risk. For example if your .Xauthority file gets the wrong permissions, you could be left unable to log in.

As other user pointed out, NTFS does not support some of the features that applications/service may need, like unix symbolic links, and then there is also the risk of fragmentation, which happens much more on NTFS than on ext file systems. For safety, stick with something like xfs, ext3/4, or even btrfs.

EDIT: Another thing I took note of, you said you used wubi to install on an NTFS partition. This only works because it creates a virtual disk, but as I mentioned above, fragmentation can occur. If you put your /home folder on a partition under the control of windows there is a risk of corruption (I don't have links, but I have experience; I've done something similar before, and had to do a disk check every time windows accessed the drive. Little did I know that windows was messing things up slowly but surely).