You can create an IPSec policy to filter all inbound/outbound traffic on a
machine or a domain, or to configure a site-to-site connection like you
would use for a VPN. IPSec is a huge topic, entire books can (and have)
been written about it. This KB should get you started: http://support.microsoft.com/default.aspx?kbid=816514,
For additional tutorials and help beyond that, do a Google search for:
Windows Server 2003 IPSec filtering
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