The Space Quest games are the best ever for this. My favorite was Space Quest III. This game included a menu option called "Boss Key." (This game had menu buttons across the top of the screen, labeled File, Edit, Etc.) When you hit "Boss Key," the game berated you for playing the game while you were at work and refused to give you an excuse to give to your boss. There were other little homages - the Starship Enterprise warps away from Monolith Burger (a combination of McDonald's and the monoliths from 2001) the first time you arrive, you get chased by a terminator, and the scrap in the garbage frigate includes a TIE fighter, Optimus Prime's head, and the nose cone from the spaceship from the Tintin "Explorers On the Moon" story.
EDIT: my favorite easter egg ever is probably from Max Payne. There's a level - I think it's when you're chasing Vinnie Gognitti - when you get on an elevator and this really awful elevator muzak starts playing. The speaker is in the top of the elevator; if you shoot it, Max thanks you exasperatedly.