The Skull-and-Bones Society (on which this movie was based) actually gives out watches to each class of skulls, though not necessarily with the whole branding ceremony. After the movie was filmed, Joshua Jackson acquired one of the actual watches and gave it to director Rob Cohen.
Hill Harper's character, Will, who plays Luke's roommate in the film, is modeled after director Rob Cohen's real-life Harvard roommate.
Yale is never mentioned by name during the film, but there are plenty of references: - At the boat race, every team is mentioned by its school name, except for "The Bulldogs." (They're the Yale team.) - The characters wear Ys on their sports uniforms. - The Skulls are said to have "322 alumni worldwide." The Yale secret society Skull & Bones uses the number 322 as an identifier on many of its symbols. - The characters are seen celebrating at a pizza parlor they refer to as "Mory's," drinking from a big golden cup. Mory's is an actual place, and the tradition with the song and the big golden cup is accurate; however, it's a formal restaurant, not a pizza parlor, and actual Mory's cups are traditionally silver. - The new Skulls are sent to raid "Snake & Skeleton." There is a Yale secret society called "Book & Snake." - Some campus shots seem to purposefully mimic Yale buildings. There's a tower that looks a lot like Harkness Tower, and the dining hall looks like the one in Saybrook College.
When the Skulls members are heading out to the island, the castle in the background is Singer Castle on Dark Island. The island that the Skull and Bone Society owns is called Deer Island. Both islands are in the Thousand Island of the St. Lawrence River.