Like someone mentioned, Conker's Bad Fur Day and Live & Reloaded do this a lot. Conker says things like "Now this is what I call a platform game!", and when you don't touch the controller for some time, Conker looks toward the camera and says "Hey, stop doing that, it'll make you go blind!".
Jazz Jackrabbit 2 has a similar effect, as Jazz will start asking where you are if you don't touch the keyboard for too long.
Metroid Prime 3: Corruption has it, as Samus holds her thumb up to the player after completing the game.
Super Paper Mario does it more implicitly. When characters explain the controls by mentioning buttons on the Wiimote, Mario won't understand it, and they will say something like "Don't worry, the great being in control will understand". Very funny effect.
I also recall the Banjo games doing it at occasions, but I can't recall what exactly. In fact, Rare games in general have a habit of breaking the fourth wall. It fits with the British humour.
And I don't know if it counts, but in the FPS Shadow Warrior, at one point you enter a level and a rocket will hit in the distance in a similar fashion as in Duke Nukem 3D (a FPS by the same makers), and the protagonist will say "Hoho! Look like Duke Nukem!"
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