Sometimes they're just there for show, sometimes you can actually flush them...and sometimes, if you're lucky, you can actually "use" it.
Toilets as a Game Mechanic
In the The Sims franchise of games, one of the needs of the Sims that needs to be catered to is 'Bladder'. Bladder, which increases slowly with the passage of time and quickly when the Sim eats, can only be relieved through the Sim using a toilet. There is a range of toilets which can be purchased and installed into the Sims' homes for that purpose. Female Sims can also get morning sickness and go to the toilet to vomit.
In the beginning of the game, Prey, the player can stand over toilets and flush them by pressing the action button. You can hear and even see the water flushing down the drain. True flushing physics.
In Duke Nukem 3D, using the toilet occasionally restores ten health points. In Fallout 3, drinking from a toilet restores health, but increases the player's radiation level, with the exception of the toilets in Tenpenny's room, the Tranquility Lane simulation, or Vault 101. In No More Heroes, using the toilet in the main character's apartment serves as the save point for the game.