As a consultant, I am often faced with an unfamiliar Linux system (usually RHEL). I always find it useful to understand which files that shipped with rpm packages have been modified, since it's usually a good indicator of what customizations have been performed on the system. To determine the modified files, I simply run:

  % rpm -qa | xargs rpm --verify --nomtime | less

  # Sample output:

  missing     /usr/local/src
  .M......    /bin/ping6
  .M......    /usr/bin/chage
  .M......    /usr/bin/gpasswd
  ....L...  c /etc/pam.d/system-auth
  .M......    /usr/bin/chfn
  .M......    /usr/bin/chsh
  S.5.....  c /etc/rc.d/rc.local
  S.5.....  c /etc/sysctl.conf
  S.5.....  c /etc/ssh/sshd_config
  S.5.....  c /etc/updatedb.conf

The following is taken from the rpm man pages (Verify Options section):

  c %config configuration file.
  d %doc documentation file.
  g %ghost file (i.e. the file contents are not
    included in the package payload).
  l %license license file.
  r %readme readme file.

  S file Size differs
  M Mode differs (includes permissions and file type)
  5 MD5 sum differs
  D Device major/minor number mismatch
  L readLink(2) path mismatch
  U User ownership differs
  G Group ownership differs
  T mTime differs

Using this trick, I can quickly determine what configuration files have been modified as well as any metadata modifications (ownership, link etc.).