Black Magic Script taken from http://unix.stackexchange.com/questions/49959/how-to-restore-default-group-user-ownership-of-all-files-under-var, adapted for /usr and fixed (there was a typo in on of the sed commands). Be careful with this!

fix_permissions.sh

#! /bin/bash

perm_string_to_mode() {
  string="$1"
  let perms=0

  [[ "${string}" = ?r???????? ]] && perms=$(( perms +  400 ))
  [[ "${string}" = ??w??????? ]] && perms=$(( perms +  200 ))
  [[ "${string}" = ???x?????? ]] && perms=$(( perms +  100 ))
  [[ "${string}" = ???s?????? ]] && perms=$(( perms + 4100 ))
  [[ "${string}" = ???S?????? ]] && perms=$(( perms + 4000 ))
  [[ "${string}" = ????r????? ]] && perms=$(( perms +   40 ))
  [[ "${string}" = ?????w???? ]] && perms=$(( perms +   20 ))
  [[ "${string}" = ??????x??? ]] && perms=$(( perms +   10 ))
  [[ "${string}" = ??????s??? ]] && perms=$(( perms + 2010 ))
  [[ "${string}" = ??????S??? ]] && perms=$(( perms + 2000 ))
  [[ "${string}" = ???????r?? ]] && perms=$(( perms +    4 ))
  [[ "${string}" = ????????w? ]] && perms=$(( perms +    2 ))
  [[ "${string}" = ?????????x ]] && perms=$(( perms +    1 ))
  [[ "${string}" = ?????????t ]] && perms=$(( perms + 1001 ))
  [[ "${string}" = ?????????T ]] && perms=$(( perms + 1000 ))

  echo $perms
}

# generate a list of installed packages that have files etc in /usr
grep -l /usr/ /var/lib/dpkg/info/*.list  | \
  sed -e 's:/var/lib/dpkg/info/::' -e 's/\.list$//' | \
  xargs dpkg -l | \
  awk '/^[hi]/ {print $2}' > /tmp/packages.list

# clean out the apt cache, so we only have one version of each package
# apt-get clean

# download the packages as if we were going to reinstall them
# NOTE: packages which are no longer available for download
# will not have their permissions fixed.  apt-get will complain about
# those packages, so you can get a list by redirecting or tee-ing the
# output of this script.
xargs apt-get -y -d -u --reinstall install < /tmp/packages.list

for pkg in $(cat /tmp/packages.list) ; do
   PKGFILE="/var/cache/apt/archives/${pkg}_*.deb"

   if [ -e $PKGFILE ] ; then

     dpkg-deb -c /var/cache/apt/archives/${pkg}_*.deb | \
       awk '/\.\/usr\// {print $1, $2, $6}' | \
       sed -e 's/ /\t/' -e 's/ /\t/' | \
       while IFS=$'\t' read permstring ownergroup filename ; do
          # don't change owner/group/perms on symlinks
          if ! [[ "${permstring}" =~ ^l ]] ; then
            mode=$(perm_string_to_mode $permstring)
            # change "owner/group" to "owner:group" for chown
            ownergroup=${ownergroup//\//:}
            # remove leading '.' from filename
            filename=${filename#?}
            chown "$ownergroup" "$filename"
            chmod "$mode" "$filename"
         fi
       done
     echo
   fi
done