I decided that I wanted to run a vpn server for ease of use. I got PPTPD running and I was able to connect to it via the PPTP client. Then I figured I'd move to something open-source, so I chose OpenVPN.

The only VPN experience I have is with Microsoft VPN servers, so I expected a window to open up with the other desktop on it.

Can someone explain to me how the non-Microsoft VPNs work differently and what I need to use a desktop remotely through the VPN?

Hello there. First of all, you should know that there's a difference between a VPN and a Remote Desktop. A VPN is used, mostly, to access servers (or networks) over a network (usually, the internet). The Remote Desktop protocol (such as Microsofts RDP, Terminal Services, Linux X11 Remote Desktop, and so on) is used to access another computer's "desktop", be it an active session, as in Windows Assistance, or a new session in an X11 server.
Hence, a VPN and a Remote Desktop are two completely different things, and although the usual procedure is to access a Remote Desktop on a network over a VPN, this is not necessary mandatory. Please, let us know what do you want to do and through some light on the scnenario you're using (ie: access a server from another office branch, access your office desktop from your house, etc).
Regarding the difference between VPN protocols.. most of them are in the protocol itself and in the software used. You can't access a PPTP VPN Server with an OpenVPN client, or access a FreeSWAN Server with a Cisco VPN client.

Thanks for the info, Walruz.

I figured that that was the case, but I didn't know where to go after I got things connected. Everything I've found on the Internet doesn't discuss much past simply installation and configuration and making the actual connection.

Basically, all I'm wanting to do is to vpn into my machine I use as a file server. I usually SSH in, but sometimes it's nice to have a GUI when you're moving files around a lot. So I want to be able to log in and use a desktop environment.

Once I get this sorted out on my home network, it's a snap to forward the right port/s to the server so I can do the same when I'm away from home. It's just a convenience, really. I'm open to just about any method that will allow me to do this securely.

So, basically, I have two machines sitting next to each other on a network, one as a VPN server and the other acts as the client.

Well.. as for moving files through a GUI, the solution can be using SCP. Putty PSCP or Midnight Commander on Linux, or WinSCP on windows.

Now.. if you want to use a Desktop environment, the solutions can be
- VNC (link here)
- X11 Remote desktop (on Gnome 2.2 this feature is easily accesed through the System/Preferences menu.. KDE or other DM may have its differences)

As you can see.. a VPN is overkill for this tasks since you don't need it at all if both computers are on the same network. On the other hand, if you're going to do this over the internet, an encrypted VPN or a SSH Connection is the answer (but in the end, you'll be using SCP or a Remote Desktop protocol app OVER the link created by the VPN or SSH connection).

Hope this helps