Gentoo remounts all filesystems read-only, while killing processes at the same time. (FUSE doesn't support the remount option though) I tried a workaround, which requires quite a lot of reordering in the rc.shutdown script. It works, but spews quite some messages. Also, it doesn't care about the fact that some processes being killed might want to write data somewhere.

for i in $(cat /proc/mounts | grep ^/dev/.d. | cut -f 1 -d ' ')
do
mount -n -o remount,ro $i || umount -n $i
done

The Gentoo solution is complex, and available here:
% wget -O - http://dev.gentoo.org/~uberlord/baselayout/baselayout-1.13.0_alpha9.tar.bz2 | tar xjf - sh/rc-services.sh init.d/halt.sh

Until I can think of a good fix, please umount your ntfs volume in /etc/rc.local.shutdown (create the file if it doesn't exist, begin it with #!/bin/sh as any shell script and make it executable).

Thanks for the hint about rc.local.shutdown. Perhaps it will be a good idea to include this file in the same way as rc.local in the initscripts package. Better will be that the file includes a comment about unmounting fuse mounts at this place.

A second candidat for rc.local.shutdown could be this removing of the psmouse module because for me this is a custom and not a system wide variable. So good it could be for laptops in my case with this line the light of my optical mouse is even on after shutdown the pc. So i even have to comment out this line which is not bad but handling such custom things in the same way as with rc.local would be more logical. But if nobody else have this problem forget the second paragraph.

I agree. Having rc.local.shutdown (no matter empty or prefilled with some (commented, of course) most used commands) will be useful. Because now most users even don't know about the possibility to use rc.local.shutdown.

Guys, try this:
Edit /etc/rc.d/netfs, there is this line:
umount -a -t nfs,smbfs,codafs,cifs,shfs,fuse
change it to
umount -a -t nfs,smbfs,codafs,cifs,shfs,fuse,fuseblk
Don't forget to add the netfs DAEMON in rc.conf. See if that umounts ntfs-3g early.

Can we get some information about the status of this bug? The FUSE package doesn't contain an rc.d script right now. If a workaround is needed, is it recommended to umount in rc.local.shutdown?

I have "umount -a -t fuseblk" in rc.local.shutdown to be on the safe side, maybe the above change should go to rc.d/netfs

Fixed in initscripts-0.8-9 by adding fuseblk support to rc.sysinit and netfs.
Mounting/umounting of these filesystems are hadnled by netfs initscript:
nfs,smbfs,codafs,cifs,shfs,fuse,fuseblk