How about Baten Kaitos? In it and its prequel, you are a character in the game. As in YOU, dude with the controller; you're a extradimensional guardian spirit who helps guide the main characters through the game. Often times the party will turn towards the camera and ask, "What do you think we should do, (insert name here)?"
It's always done seriously, and I suppose it's not technically breaking the fourth wall because you could be considered merely an\ actor in the story.
Also, I'll admit that some of the answers don't actually affect the story; the characters take the left path even though you suggested right. Luckily though, answering "right," i.e. in a way that pleases the designated hero, increases your luck in battles because you and the hero are in sync with one another.
Really, I'm surprised I'm the first to mention this.