Many of the Gotham Rogues are played by members of the Pittsburgh Steelers. Ben Rothlisberger and Hines Ward can be seen during the pan of the team during the National Anthem. The game is also being played at Heinz Field, home of the Pittsburgh Steelers.
Comedic actor Thomas Lennon has a small role as the doctor Bruce sees for a check-up before he visits Gordon. Lennon previously played a similar role in director Christopher Nolan's "Memento" (as the doctor the character Sammy Jenkis visits). Lennon stated that Nolan specifically wanted him for the role of the doctor in this film, and has speculated that perhaps Nolan considers them to be the same character.
John Blake talks about "giant alligators" being in the sewer, likely a nod towards Batman villain Killer Croc.
In the scene where John Blake visits Bruce Wayne in his mansion, you can see a bust of C-3PO behind Blake and to his right. As Blake gets up to leave, you can see the bust in greater detail.
There is a subtle tribute to one of the film's graphic novel inspirations, "The Dark Knight Returns" by Frank Miller (1986). In both the 2012 film and 1986 graphic novel when the Gotham Police Department are pursuing Batman, the veteran policeman offers some advice. The line spoken by the veteran policeman to the younger policeman in the film ("Oh boy, you're in for a show tonight, son.") is a nod to the line said by the veteran policeman in "The Dark Knight Returns" ("We're in for a show, kid.").