In the sewers of Sapienza there's a reference to the Super Mario Brothers series. If the player travels throughout the sewers long enough they'll come across two plumbers, one in a red uniform and the other green. Their names are Mario Salvatore and Luigi Salvatore (the player can see their names in Contracts).
In Sapienza, while wearing the Plague Doctor disguise, there is a wine bottle that can be shot near the escape boat that will drop a key to the sewers. When you get to the sewers you will find skeleton hands coming out of the ground of the catacombs.
If you dismiss all soldiers in the school in Marrakesh while wearing the Officer disguise and then proceed to the radio room in the school, turn on the intercom, and then the radio, a song will play throughout the school causing every soldier, including your target Reza Zaydan, to dance.
If the player infiltrates the auction without a disguise, Agent 47 will introduce himself to the target as Tobias Rieper, an alias he used throughout other Hitman games in the series.
If you go into Rocco's Apartment in Sapienza there's a computer with the Hitman Sniper Challenge title screen on it. Rocco was portrayed by the #1 player in the Hitman: Sniper Challenge, and was included in the game as a reward.