Please also make sure you never used moveroot.sh scripts that are floating all over the internet. These scripts used to move files from /usr/lib and /usr/share to some place like /home/usr/lib and /home/usr/share. These folders are also blindly used by nitdroid as part of its system.
If you remove those your e.g. locale settings will get screw badly. Well there are ways of rebuilding those, but finding these information on talk.maemo.org depends toomuch on luck than on search skills