In the cold open, when Barney is beckoned into the alley by a man in a fez, behind them is a sign reading "DUK TAI TRADING COMPANY," an obvious reference to his duck tie, the disappearance of which the scene is meant to explain.
In the cutaway scene with Lily and Marshall in the bathtub, Lily is reading a book titled "Pamela Was Robbed." This is likely referencing director Pamela Fryman's loss in the Outstanding Directing category at the Prime Time Emmy Awards (for the episode "Subway Wars").
The opening Barney action sequence contains a couple of nods to Indiana Jones: the man wearing the fez in the alley and the rescuing of the young boy referred to by Barney as "the kid".
In the opening sequence, the roof Barney ascends is the same roof where he and Marshall previous conducted their "conference calls" when the two were co-workers at Goliath National Bank.
In this episode, Barney claims that he is older and taller than Ted. Ted denies that Barney is taller, but agrees that he's older. In real life, Neil Patrick Harris is a year older than Josh Radnor, and the two men are the same height.