Noticed this when the boot-time took too long. Every reboot the journal must recover the root file system (i have the /home-filesystem on a second partition). I saw this in dmesg (not always the same but about, and this is always there at every boot):
[ 9.252087] EXT3-fs (sda1): recovery required on readonly filesystem
[ 9.252091] EXT3-fs (sda1): write access will be enabled during recovery
[ 10.928126] kjournald starting. Commit interval 5 seconds
[ 10.928181] EXT3-fs (sda1): orphan cleanup on readonly fs
[ 10.928188] ext3_orphan_cleanup: deleting unreferenced inode 338285
[ 10.928222] ext3_orphan_cleanup: deleting unreferenced inode 337758
[ 10.928229] ext3_orphan_cleanup: deleting unreferenced inode 338428
[ 10.928238] ext3_orphan_cleanup: deleting unreferenced inode 1622019
[ 10.936544] ext3_orphan_cleanup: deleting unreferenced inode 1622017
[ 10.936559] EXT3-fs (sda1): 5 orphan inodes deleted
[ 10.936562] EXT3-fs (sda1): recovery complete
[ 11.017444] EXT3-fs (sda1): mounted filesystem with ordered data mode
[ 31.210636] Adding 3903788k swap on /dev/sda2. Priority:-1 extents:1 across:3903788k
[ 32.044232] EXT3-fs (sda1): using internal journal
I have tried much of the workarounds covering dbus bugs or network-manager bugs for example https://bugs.launchpad.net/ubuntu/+source/dbus/+bug/740390 to no success. My system is a stock ubuntu 12.04 with some PPA-packages but not system ones. I've no slight idea what happens.
Well one needs to find out which files were still held open. As far as I know that late at shutdown, there is no libnih activity left.