I'm sure that we've all wondered while playing a game, "where's the bathroom here?" When a game actually has facilities, it adds a bit of respect for reality, at least to me.
I'll get the list started:
Earthbound
Metal Gear Solid, 2, 3 (though not MG1 or 2, as far as I know)
Final Fantasy 7
Sam & Max Hit the Road (it's part of a puzzle too!)
Goldeneye 007
Breakdown
What others?