These are some of the most disturbing I've seen:
Salo (1975) - Ahhh Salo. It's a classic.
Irreversible (2002) - the 10 minute rape scene *shudder*
Dumplings (2003) - it's just a messed up theme
Men Behind the Sun (1988) - frightening look at reality
August Undergrounds Mordum - you just know people are out there doing things like this
Visitor Q (2001) - f**ked up
Strange Circus (2005)
I Spit on Your Grave
Antichrist
Human Centipede
Storytelling
Palindromes
Then you have the usual Cannibal Holocaust, Happiness, Clockwork Orange, Kids, Oldboy, Audition.........................
I liked the movie Freaks (1932). Not so much disturbing as much as bizarre. Gummo (1997) was a little messed up. I agree with the postee who said Harmony Korine movies...love 'em.