I believe there was one in Half-Life 2 where there was a half-eaten torso or a dead headcrab in it, not to mention no toilet in the apartements has water in them, gross if someone went in one by accident.
Also in Doom 3 there's a toilet where when you open it there is a corps sitting there...but wait, OH its a zombie and now he's trying to eat your face. Also there's a part where you look in one of the bathroom mirrors and see a vision of hell behind you. I knew public bathrooms were vile places but come on.