Keep Remote Directory Up-to-date

How "real-time" do you want the syncing? I would still lean toward rsync since you know it is going to be fully supported on both platforms (Windows, too, with cygwin) and you can run it via a cron job. I have a super-simple bash file that I run on my system (this does not remove old files):

#!/bin/sh
rsync -avrz --progress --exclude-from .rsync_exclude_remote . remote_login@remote_computer:remote_dir    

# options
#   -a  archive
#   -v  verbose
#   -r  recursive
#   -z  compress 

Your best bet is to set it up and try it out. The -n (--dry-run) option is your friend!

Keep in mind that rsync (at least in cygwin) does not support unicode file names (as of 16 Aug 2008).

lsyncd seems to be the perfect solution. it combines inotify (kernel builtin function which watches for file changes in a directory trees) and rsync (cross platform file-syncing-tool).

lsyncd -rsyncssh /home remotehost.org backup-home/

Quote from github:

Lsyncd watches a local directory trees event monitor interface (inotify or fsevents). It aggregates and combines events for a few seconds and then spawns one (or more) process(es) to synchronize the changes. By default this is rsync. Lsyncd is thus a light-weight live mirror solution that is comparatively easy to install not requiring new filesystems or blockdevices and does not hamper local filesystem performance.