I have a bike rack on my car, and I do what I really like when others do:

1) I drive as respectfully as I can...a wide margin out and around, or if I am in the oncoming lane, I get way over to my side to give oncoming traffic lots of room to go around the cyclist, etc.

2) If I have time, I stick my arm out the window with a thumbs up sign.

I know that when I'm riding, I hate any kind of honk...the cheerful kind, too, really. When I see a car give me a LOT of room, especially a car that has a bike rack, and especially a car that will just get the heck around me (not go super slow just behind me forever), I know they are sympathetic without any special wave or honk.