Here is a little perl script (big thanks to the original author) that will list all mailboxes on the server that returns the following fields, tab-separated:
user, email address, mailbox size (unit: MB)

opendir(USERS, ‘/var/cpanel/users’) || die $!;
while (my $user = readdir(USERS)) {
  # user loop
  next if $user =~ /^\.|system/; # skip . and .. dirs
  if (opendir(ETC, “/home/$user/etc”)) {
    while (my $domain = readdir(ETC)) {
      next if $domain =~ /^\./; # skip . and .. dirs
      if (-d “/home/$user/etc/$domain/”) {
        if (opendir(MAIL, “/home/$user/mail/$domain/”)) {
          while (my $email = readdir(MAIL)) {
            next if $email =~ /^\./;
            if (-d “/home/$user/mail/$domain/$email/”) {
              print “$user  $email\@$domain  “;
              system(“du -BM –max-depth=0 /home/$user/mail/$domain/$email/ | cut -f1”);
              }
            }
          }
        closedir(MAIL);
        }
      }
    closedir(ETC);
    }
  }
closedir(USERS);