I nod in whatever way I think will be seen by the other rider at the time, so sometimes it's down and to the right sort of 'wink' style, other times it's a definite forward nod. If the road's straight enough and it's safe then I'll give a nice big wave too.
If it's a Harley rider I wave, nod, shake my legs, anything to get them to notice me and guilt-trip them into waving / nodding back!!
And finally, if I've just passed a 'safety' camera van, I'll give a nice clear thumbs-down with either hand to notify oncoming riders that they are about to enter a potential accident black-spot!