Simple backup script in Python
This program is really a pleasure to read. It accomplishes the desired outcome neatly and succinctly. The only thing I could think of that might be an improvement is threading. Other than that this program looks fantastic.

I can see where making this program threaded can be a great benefit when dealing with smaller files. I'm not sure, but I fear with larger files or smaller buffering, having this program run copy routines in parallel might bring the system to a halt. I wrote up a minor modification to your excellent source code to illustrate my idea:

""" Simple backup script which just creates the root structure in an other
folder and syncs everything which recursevely lies within one of the source
folders. For files bigger than a threshold they are first gziped."""

import argparse
import gzip
import os
import shutil
import sys
import threading

def parse_input():
    parser = argparse.ArgumentParser()
    parser.add_argument('-target', nargs=1, required=True,
                        help='Target Backup folder')
    parser.add_argument('-source', nargs='+', required=True,
                        help='Source Files to be added')
    parser.add_argument('-compress', nargs=1,  type=int,
                        help='Gzip threshold in bytes', default=[100000])

    # no input means show me the help
    if len(sys.argv) == 1:
        parser.print_help()
        sys.exit()

    return parser.parse_args()


def size_if_newer(source, target):
    """ If newer it returns size, otherwise it returns False """

    src_stat = os.stat(source)
    try:
        target_ts = os.stat(target).st_mtime
    except FileNotFoundError:
        try:
            target_ts = os.stat(target + '.gz').st_mtime
        except FileNotFoundError:
            target_ts = 0

    # The time difference of one second is necessary since subsecond accuracy
    # of os.st_mtime is striped by copy2
    return src_stat.st_size if (src_stat.st_mtime - target_ts &gt; 1) else False

def threaded_sync_file(source, target, compress):
    size = size_if_newer(source, target)

    if size:
        thread = threading.Thread(target=transfer_file, 
                                  args=(source, target, size &gt; compress))
        thread.start()
        return thread

def sync_file(source, target, compress):
    size = size_if_newer(source, target)

    if size:
        transfer_file(source, target, size &gt; compress)


def transfer_file(source, target, compress):
    """ Either copy or compress and copies the file """

    try:
        if compress:
            with gzip.open(target + '.gz', 'wb') as target_fid:
                with open(source, 'rb') as source_fid:
                    target_fid.writelines(source_fid)
            print('Compress {}'.format(source))
        else:
            shutil.copy2(source, target)
            print('Copy {}'.format(source))
    except FileNotFoundError:
        os.makedirs(os.path.dirname(target))
        transfer_file(source, target, compress)


def sync_root(root, arg):
    target = arg.target[0]
    compress = arg.compress[0]
    threads = []

    for path, _, files in os.walk(root):
        for source in files:
            source = path + '/' + source
            threads.append(threaded_sync_file(source, 
                           target + source, compress))
#            sync_file(source, target + source, compress)
    for thread in threads:
        thread.join()


if __name__ == '__main__':
    arg = parse_input()
    print('### Start copy ####')
    for root in arg.source:
        sync_root(root, arg)
    print('### Done ###')