I totally misunderstood you. I though you were talking about replacing graphics with any other output method, as in games for blind people! Then laremere is right. The sense of smell in Twilight Princess is a nice example.
Both are fine, but I am after games that make these alternative outputs, either actual senses or simulated through others senses, as important as normal sight, even if just temporarily. Many games have simulated senses, like the simulated pain, which is very common in FPSs now, but they are secondary, in the sense you know where you are and what is around you without them.
Another, very short example is the echolocation used in a very small part of Castlevania: Symphony of the Night. You are unlikely to be able go through a specific tunnel without the "Echo of the Bat", since it is completely dark and filled with spikes. The echo appears as a cone projected by the main character's mouth(while turned into a bat). This cone clears temporarily the darkness inside it and bounce of walls.