I would use rsync for this purpose. You can download a Windows-compatible binary or get it as part of Cygwin (I recommend the former approach unless you already have Cygwin installed). You can either push files to the remote site or pull from it. I prefer the pull method, but either will do.
Using the pull method, the rsync daemon will run on the source server; using push, the rsync daemon will run on the destination server. Here's an example of a pull daemon config file:
max connections = 4
port = 873
read only = true
write only = false
auth users = syncman
secrets file = /etc/rsyncd.secrets
strict modes = false
hosts allow = 192.168.1.8
refuse options = delete
[ProjectOne]
comment = Jimmy's Project
path = C:/projects/project_one
[MutualProject]
comment = The MUTUAL project
path = C:/paid_projects/mutual
How you specify the path will depend on which rsync port you use (e.g. cygwin specifies paths like this: /cygdrive/c/projects/project_one). You would then issue this command from the server:
rsync -a -v 192.168.1.15:ProjectOne backups/ProjectOne
(where the IP address is the source machine's IP address). If the backup server is a Windows box, you would need one of the many cron-for-windows implementations.