I drive a motorcycle as well as my Bimmer and most motorcyclists will give a small wave out of courtesy. It's a bit tougher in a car though. I think a little flash of the lights might be more appropriate than trying to roll down the window and wave every time you see another Bimmer. Good idea though. It's like the Bimmer Brotherhood.
NOTE: I hate to say that there are a lot of BMW drivers who are, well...uh...let's just say they're not exactly car enthusiasts (ie, the 40 year-old housewives driving the 750iL's and X5's that almost run me off the road on my motorcycle).
That said, they might not get it. Good luck!
2002 BMW 325i