I know it's a little late to be posting this, so I'm not going to write a lot about it. I am surprised how many references to animal cruelty the show BONES contains. It's nice to see a mainstream and popular program to shed light on animal cruelty and shed positive light on activists who fight against it.
One episode involved someone using a stun gun to kill someone. When agent Booth asks Dr. Brennan, "Who could do this to somebody?"
Dr. Brennan replies, "Who could do this to a pig?"
In one episode a murder takes place inside of a chicken factory farm. There are activists protesting the cruelty and abuse of the chickens, when Booth (who is the strong masculine male character) sees the inside of the facility he makes reference to understanding why the activists are upset. The episode contains images of animal cruelty taken from real life factory farms, and some of the characters are disturbed. The murderer does not turn out to be any of the activists but I won't ruin it for you.
There are more references through out the series, I would assume this has a lot to do with Emily Deschanel being a vegan in her real life.