It hasn't happened to me very often. (Running for 38 years) I guess the Bay Area doesn't have that many clowns.
But, when I was younger the few times it happened I responded by flipping them off. I was once a hot head always willing to fight.
I learned growing up that a willingness to fight was a great asset. I believed that there was no such thing as a fair fight and would use anything available as a weapon, including my teeth. My approach was to inflict as much serious damage as possible as fast as possible. Even large guys fear speed.
Now that I'm older, and not as much of an ego maniac, I don't take things like that personally. It's just some jerk yelling at an anonymous runner. I just happen to be that anonymous runner, it could have been Brad Pitt or Joe Montana that the clown was heckling, what difference does it really make.
As far as the guy who says he just smiles and waves...you're an effeminate loser. You're not fooling anyone.