Scott Pilgrim & The Infinite Sadness
In a strip by David McGuire in the third volume of the Scott Pilgrim comic, Ramona mentions "Donkey Kong".
Additionally, the fact that Ramona fights using a hammer in this comic is considered by some a reference to the Hammer power up from Donkey Kong, but it is more likely just a generic heavy weapon. She retains the hammer in the Scott Pilgrim movie and videogame.
Scott Pilgrim's publisher Oni Press, didn't held any right over Nintendo's Donkey Kong, but they only included a minor reference.