There are MANY ways to do this. I am not sure whether you are backing up
linux --> windows
windows --> linux
You could do both methods using rsync and SAMBA.
Just run SAMBA on your linux server, share something like "/backup." or if you need too /.
Or if you are backing up a windows machine mount the windows machine's SAMBA shares on the linux machine.
Rsync the two directories. (You can use Rsync locally)
Be sure to lock down samba, this might be the one flaw in this system, it should preferrably only listen on a private network so there is no fear of outside exploitation.
If you want a simpler technique, just use SCP and copy the files across, I believe you can get a basic SSH server for windows 2k so this would work in either direction.