These are two of the more widely known ones, but both Birdo and Vivian (Vivan appeared in Paper Mario 2) are male in the Japanese version of the Mario franchise.
I'll try to come up with some more, stuff like this is kind of fun.
Edit: Wait, wait, I have a REALLY trivial one, but it's fun nonetheless. In the Xbox 360 version of Lego Star Wars: The Complete Saga, the achievement "Did I Break your Concentration?" which is unlocked by killing the Emperor with Mace Windu, is a reference to the film Pulp Fiction, as Samuel L. Jackson played characters in both films (Mace Windu in Star Wars) and the title of the achievement was a line he spoke in Pulp Fiction.
Man, that one was really obscure. Hahaha.
I'll try to come up with some more, stuff like this is kind of fun.
Edit: Wait, wait, I have a REALLY trivial one, but it's fun nonetheless. In the Xbox 360 version of Lego Star Wars: The Complete Saga, the achievement "Did I Break your Concentration?" which is unlocked by killing the Emperor with Mace Windu, is a reference to the film Pulp Fiction, as Samuel L. Jackson played characters in both films (Mace Windu in Star Wars) and the title of the achievement was a line he spoke in Pulp Fiction.
Man, that one was really obscure. Hahaha.