Assassin's Creed 2
November 17, 2009
In Assassin's Creed 2 there's a character named Mario Auditore, who's the uncle to Ezio Auditore, the game's protagonist. When met for the first time in the game, he introduces himself by saying "It's-a me, Mario!" referencing the same line spoken by Nintendo's Mario in many occasions, first heard in the title screen of Super Mario 64.
Assassin's Creed: Brotherhood
November 16, 2010
Additionally, in the mission "Femme Fatale", after Ezio grabs Lucrezia Borgia to drag her toward Caterina Sforza's cell, she comments:
Rescuing princesses from castles now?
This is believed by some to be a reference to the Mario series, where Mario has to save Peach from a castle, however, since it wouldn't make sense for a fifteenth-century person to make a videogame reference, this is more likely just a reference to classic fairy tales. Basically there's nothing suggesting the developers specifically referenced Mario in the sentence rather than a generic tail of a hero saving a princess.
Assassin's Creed's company Ubisoft don't have any right over Nintendo's Mario, but they only included minor homages to that series.