Conrad H. Roth has a blog called Varieties of Unreligious Experience. On it you can find everything you ever wanted to know about the history of the head nod and more and more (the best was saved for last I believe). Parts one and two are largely etymological speculations. Part three treats the gestural aspect. Why he chose the humble nod, I cannot tell, but he provides ample reading material on the subject.

“Proud day: Rice accepts Bush’s nod to head State” (source MSNBC)

A possible candidate for gesture mix-ups is the way Bulgarians nod for yes and no (see video). I hope the people of Umanify are still listening? (They wanted their avatar to use appropriate head gestures)