I'm amazed nobody's named Phantasmagoria 2 (A Puzzle of Flesh), which has a HUGE number of Easter eggs. Not only that, but once you find one of them, it starts keeping score. I've done a few, but didn't want to spoil the atmosphere by going through all of them. One of these days I'll have to play it through again and do them all!
Here's a list of all of them.