Difficult to wave a thank you most times. With vehicles as public enemy #1, we mostly deal with their jack**s maneuvers.
On nearly every ride, however, I wave motorists thru intersections (when they deserve right-of-way) or when I judge it safe for them to pull out before my arrival.
It never does any good to get angry and give them the finger. They could be packing or they may circle back to zap me.