Hodgins and Zack throwing the frozen pig through the wood chipper is the beginning of the long-standing plot line / joke of Hodgins conducting unorthodox (and often unapproved) experiments to not only collect data, but for the fun of it.
This woodchipper case closely resembles that of Helle and Richard Craft. Richard Craft murdered his wife Helle in their bedroom, then froze her body in their icebox in the garage. He then replaced the carpet all over their house and took his dead wife's body to a nearby river. There he dismembered her body with a chainsaw and ran the parts through a woodchipper he rented. Doctor Henry Lee was the lead forensic scientist on the case. This was the subject of the very first episode of the very famous (and long running) crime documentary series, Forensic Files.
Booth looks through the file of Bones' parents. He looks at a picture of them. The male isn't Ryan O'Neal who, later on in the series, portrays her father. This is explained by them saying he had plastic surgery so he wouldn't be recognized (his own daughter doesn't recognize him either.)