AJ and Houdini are both microchipped, though I wasn't around when they were microchipped. I had my pups, Myrl and Levi, microchipped as soon as I got them. Levi didn't seem bothered by it (he acted like the vet had poked him and wanted to poke back) but when Myrl was microchipped, the vet was very rough and he bled a LOT. She kind of stabbed him with the injector and he yelped and his white fur turned red. It was horrible. I wanted to stab her! But at least the vet who microchipped Levi was gentle.
I'm totally for microchipping, even with the one bad time. And I know tons of instants where microchips brought an animal back home.