The strangest one I can remember has to be in that beloved fan favourite, Metroid: Other M.
They don't serve any function other than filling out the setting, but when you approach them, the game switches to an over-the-shoulder viewpoint at a plodding walking speed for no discernible reason. They're just there. I'm not even one of those people with a chip on my shoulder about Other M, but something about the way the game draws special attention to entirely superfluous toilets perfectly encapsulates the overall experience.