I've never set up a VPN but have now been tasked with creating one on a Windows 2003 server.
What basically needs to happen is this server(which does not function as a router) needs to function as a VPN server. This is so that we can VPN into this server from across the internet. Whenever we VPN into this server we need to be capable of accessing the server and it's LAN. We also need some form of encryption through the VPN
How would I best set this up?
You can do this using the built-int Routing and Remote Access Server:
http://technet.microsoft.com/en-us/library/cc736357(WS.10).aspx
http://technet.microsoft.com/en-us/library/dd835612(WS.10).aspx
If the server isn't acting as the Internet gateway for your network, you will need to configure it to run with a single NIC (this can be done using a "custom" configuration in the RRAS setup wizard and then manually configuring the VPN server) and then you will also need to configure your Internet router/firewall to forward to your server the needed port(s) for VPN access. The actual ports you will need to forward depend on whether you are using PPTP or L2TP for your VPN.
RRAS is your best bet, here's a great place to start.