I haven't any experience in this field but I will attempt an answer anyway!
I don't think there's much point in using two LEDs.
Johnny Chung Lee uses two, but his application does not allow the head to actually turn - it only allows translation in the x and y axes, and zooming in and out. This is because when the two dots get closer together, the computer doesn't know if they are further away from the sensor or whether they have actually turned.
With three points (such a rig isn't that much more difficult to build), then you get all six degrees of freedom, as the computer is able to tell how far away the light points are, as well as their rotation.
I think all the current applications of FreeTrack are for the turning of the head, and not just for translation and zooming.
The Wii might allow more degrees of freedom using just the two IR points of the sensor bar, but then, there are a lot more sensors in the Wiimote that we are not making use of.