I found Deathwish II very unsettling for some reason. The fates of the daughter and housekeeper (especially on the Euro version, from what I've read) are so lingered over and explored, it just sets this mood of unredeeming darkness and moral decay.
The fully uncut version was finally made available on Blu-ray within the past year or two. The extra footage isn't incredibly shocking (at least by today's standards) but it's definitely a little more explicit than what we saw in the theatrical version.
I'm a huge Sidney Lumet fan, but Equus was the only film of his I've seen that I didn't really care for. The plot was just too ridiculous and unrelatable.
8mm was mentioned, it's a mildly disturbing thriller, but the premise is laughable just a few years later. 1999: "Snuff films don't exist! Let's make a movie as if they did" The Internet: "Ha! Hold my beer" Something I haven't seen mentioned yet; The Plague Dogs an animated film revolving around a pair of talking dogs that broke out of a medical research complex. I found it very disturbing as an adult, I can't imagine somebody might accidentally show this to children because it's an animated talking dog film
+1 for Don't Look Now... A great movie and please go see it if you haven't already, but for me one time is enough....
Fassbinder's film Martha (1974) about a woman who marries a sadist, is the most disturbing film I've ever seen. I don't think I could watch it again, but I can remember so many things about it.
I remember watching 'Flowers in the attic' as a child and being completely freaked out, and had a few nightmares after watching it. I'm not sure how disturbing I would find it today though.
One of his heavier deeper thinking complicated movies outside of the crime Serpico Dog Day Afternoon types. Nonetheless the psychological thriller worked for me.
Mulholland Drive deeply unsettled me as a kid. Just the other day, I caught Gore Verbinski's The Cure For Wellness, which, although definitely not at all on par with many of the other films previously mentioned earlier like Salo or A Serbian Film nonetheless had a number of truly disgusting scenes and was cinematographically and visually disturbing, without much respite, for its entire duration. I also found Nocturnal Animals to be pretty disturbing, especially the psychological turmoil instilled in the lead-up to Jake Gyllenhaal's fictional wife and daughter's kidnap and rape by malicious good ol' boys.
'Begotten' for me. A Pagan retelling of the Christ myth. The first half hour of that movie is so disturbing, I've seen hardened gore hounds who couldn't hang with it. Little known but worth a look. Very unique.
The one I've seen most recently that fits the bill would probably be Cannibal Holocaust - though honestly I'd expected that to be much worse given its reputation. Still, I felt like I needed a shower when it was over. Henry, Portrait of a Serial Killer was another one that got me bad when I saw it back in the day. In both cases, I remember thinking "Okay, that was a good movie... but I don't ever want to see it again." I have heard/read enough about Human Centipede, Serbian Film, Salo, etc. that I know I will never bother to see them. I watch films to be entertained, not scarred for life. There are film buffs out there who treat "extreme" movies like those as a metric of their "endurance" (to see how much they can "handle") but obviously I'm not one of them.