Playing devil's advocate, you could argue that waving/thanking a motorist for recognizing your right of way just reinforces the idea that you didn't really have the same right of way as cars and that they just did you a favor. But, I figure, even if they're just following the rules of the road, in their mind they *did* just do you a favor, so at least you're giving them some positive reinforcement which hopefully will lead them to continue being considerate.

It does cut both ways. I've seen cyclists doing some incredibly stupid and inconsiderate things, especially on recreational group rides, like riding 3 or 4 abreast and completely blocking the road, even when a car is behind them. Usually the driver is keeping a safe distance back and not leaning on the horn, basically being sent the message that being polite to cyclists just gets you screwed. When even another bicycle can't pass you without crossing the double yellow, you and your little social network are being jerks.