One of the best ones [imo] has already been mentioned.
the one where Kid Bruce's riding the monorail with his parents on the way to the Opera,
Kid Bruce says "Is that where you work?"
His Pops says "No, I work at the Hospital, I leave the running of the company to much... Better Men"
Kid Bruce smirks, surprised and says "Better? men"
His Pops says: [obviously being modest], "more interested men.."
looks at his wife...
The Dialog between Bruce & Alfred about fixing the autopilot was definitely a callback or homage to that scene in BB,
but the subtle one no one's mentioned yet, during Bane's speech on the tumbler, when he frees the prisoners at Blackgate, ...after reading Gordon's "The Truth about Harvey Dent" speech..
he goes on to say "blood will be spilled,etc etc.."
he also says [while they cut to a shot to them underground]
"The Police will survive, as they learn to serve true justice"
isn't the "Serve true Justice" part a nod to Ras Al Ghul in Batman Begins?"
where he says ... "If someone stands in the way of true justice, you simply walk up behind them and stab them in the heart"?