Well I'm gonna go a bit off mainstream games,
So, I'm gonna say Psychonauts deserves the gold medal.
#1 Most Disturbing has to go to "Psychonauts": "Meat Circus" level,
I found meat grinders spewing out messed up zombie rabbits highly disturbing,
not to mention the Butcher's whole appearance.
#2 Honorable Mentions still goes to "Psychonouts": "The Milkman" level,
a whole level based on the concept of Paranoia would be disturbing enough as it is,
without the whole evil girl scouts troop sideline.
#3 Classic Honorable Mentions has to go to "Weird Dreams",
a game where you have to survive a bizarre nightmare featuring,
among other things a giant cotton candy machine, flying fish and a mad little girl playing with a man eating football. Wait but that's not all, the Protagonist in the real world is actually lying in an intensive care unit, and every life you lose in the dream causes his heart rate to worsen until a game over sequence shows the patient flat lining.
I guess there are more games I can talk about, but these are the core of the disturbing gaming world.