WebDAV is probably the way to go but it has its quirks. I wouldn't recommend AFP because almost no firewall will have port 548 open by default which could cause big issues. Also, there is are some security problems like DoS which can take your AFP down pretty easily.
WebDAV (similar to iDisk) is file sharing over HTTP(s) and client needs to have just port 80/443 open to get it to work. Be careful because WebDAV doesn't offer some low level options which for example allow MS Excel file sharing between users (simultaneous writing)
On the other hand there are big issues with WebDAV on Windows, in their different versions support for WebDAV works or doesn't work and you will most likely need a third party client.
The absolutely best way is to use VPN, I would recommend Fortinet with SSL VPN but there are of course another options. PPTP is not secure enough but L2TP/IPSec/SSL VPN is the way to go.