For debian systems, this finds all files that do not belong to a package.

debian_find_orphan_files.py

#!/usr/bin/env python3
"""
Search for orphan files (files that do not belong to any package)
"""
import fnmatch
import os
import subprocess
import itertools

INCLUDES = ('/usr', '/etc', '/opt', '/lib32', '/lib64', '/sbin')
EXCLUDES = ('/var/www', '/var/tmp', '/var/log', '*.pyc')

def get_files(root):
    """
    Generate all files under the given root
    """
    root = os.path.abspath(root)
    for root, _, files in os.walk(root):
        for afile in files:
            full_path = os.path.join(root, afile)
            for exclude in EXCLUDES:
                if exclude[0] == '/':
                    if full_path.lower().startswith(exclude.lower()):
                        break
                elif fnmatch.fnmatch(full_path.lower(), exclude):
                    break
            else:
                yield full_path

def get_files_in_packages():
    """
    Generate all files in all .deb packages
    """
    output = subprocess.check_output(
        'dpkg --get-selections', shell=True, universal_newlines=True)
    lines = output.split('\n')
    packages = [line.split()[0] for line in lines if line != '']
    for package in packages:
        lines = subprocess.check_output(
            'dpkg -L {0}'.format(package),
            shell=True,
            universal_newlines=True).split('\n')
        for line in lines:
            yield line

def main():
    """ Main script """
    os_files = list(
        itertools.chain.from_iterable(
            (get_files(x) for x in(INCLUDES))))
    package_files = list(get_files_in_packages())
    orphans = list(set(os_files) - set(package_files))
    orphans.sort()
    for orphan in orphans:
        print(orphan)

if __name__ == "__main__":
    main()