I will go through long stretches without playing with new technology until I either get unbusy or get talked into figuring out how to do something remotely interesting with it. Like linking FaceTime up to a help desk database. It turns out that Apple made it a very straight forward process. Simply use a facetime handler as the prefix to a URL with the phone number of the other person (iPhone 4) or their FaceTime email address (usually with the desktop app).
For example, if my email were email@example.com then you could use the following from terminal:
Or if my phone number were 310-555-1212 (it is you know;):