I remember when playing Ocarina of Time many years ago, and when I got to the Castle Courtyard, if you look through one of the windows going into the castle, you can see portraits of Mario, Yoshi, and Bowser. Also, if you hit the window with your slingshot, a guard will appear in the window and throw a bomb at you.

In Bioshock, you can see a Pacman reference: A wheel of cheese has a wedge cut out of it (for the "mouth"), and there are a line of bullet holes beside it that are supposed to represent the pellets.

In FF VII, you can see Cait Sith in the Honey Bee Inn. If you look around through the keyhole to the Lover's Room you'll see Cait Sith hopping up and down.