My current setup is a combo of unison/sshfs/rsync.. I've been using it for quite a while at this point, and it works so well that I don't even give it any thought anymore.
I have a Media Center/Fileserver box at my house that is always on, and acts as the 'master' copy of the home directory, on all my workstations my .xinitrc/.xsession calls unison to sync my home dir with the server root as the preferred copy, then calls my WM, after my WM exits, unison is called again with the local homedir as the authoritative copy. A well-crafted ignore list is crucial, ignoring things like temporary file patterns, mozilla cache, machine-specific data, obscenely large files, etc.
I use sshfs-fuse for any of the above mentioned ignored files, sshfs allws you to mount remote filesystems locally, tunneling through ssh (or something like that).
Finally, rsync can be used to give time machine like backups. In my case, I backup to USB drive connected to the fileserver, which I only turn on when running backups.
This is for the most part Linux-only, but unison has a windows binary available, and could probably be used to sync to windows automagically.
