In Brennan's apartment, you can see a picture of her and Angela on a shelf beside her dining room table. This is actually a personal picture taken of real-life friends Emily Deschanel and Michaela Conlin which was then used on the show.
McVicars' alias while in the witness protection scheme is Steve Beers. Steve Beers is Bones' Co-Executive producer.
When Brennan uses the weapon used to kill pigs on a fence, she says "I think I just became a vegetarian." In real life Emily Deschanel is a vegetarian/vegan.
We see Brennan's apartment three times in the season: in "Pilot," in "Two Bodies in the Lab," and in "The Woman in Limbo." However, every time, her apartment looks distinctly different.
First appearance of Brennan's brother Russ