My favourite easter eggs are:
I remember playing through the first F.E.A.R. and noticing a coffee machine in an office kitchen. It had an unknown brand name on it so I checked it against the game's credits and it matched up with one of the game's artists.
My favourite, though, was playing through Deus Ex: Human Revolution and finding three sea shells on the wall next to a toilet.
I love little game dev anecdotes such as these. Interesting relics of the development process.
One of my favourites is Sonic 3D's secret level select screen: https://www.youtube.com/watch?v=ZZs2HUW9tDA