If you swim out into the ocean in the Driftwood area, once you hit the boarder where you can't swim out any further if you tilt your camera to look down into the water there is a Lionhead Studios logo on the sea floor.
During the Hideout mission of bowerstone when going to capture Nigel Ferret. You will come across a room with a silver key. At the far end of the room there is a path around the boxes to the other jail cell. In the cell is a hobbe worshiping the companion cube from portal and on the table next to the cell is a cake.
Tribute to The Legend of Zelda
In the graveyard in Milifields there will be a tombstone that reads "It's dangerous to go out alone. Take this". Your dog will bark and start digging right in front of the grave. Your prize? A powerful "Toy Sword".