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I just installed a Routing and Remote Access VPN service on Windows Server 2008, though I'm not totally sure what ports I need open for that, or what type of VPN I'm using. L2TP, PPTP?
The VPN tunnel will allow remote computers to think that they are on the same LAN or switch as the server. So you have full freedom about deciding how remote machines/users authenticate after they've negotiated and established the VPN tunnel.