Eraserhead is definitely close to the top of my list, but there is another one that has been at the very top ever since I saw it in the mid-1970s (although I’m not sure it counts under the OP’s terms, since it’s a documentary): The Act of Seeing with One’s Own Eyes, by Stan Brakhage.
It is the third in a trilogy of 30-minute silent films. The first, Eyes, dealt with the police, and the second, Deus Ex, dealt with a hospital. Now, when I say “dealt with,” I don’t mean they were what you’d normally think of as documentaries. Both were very impressionist: A closeup of a hand on a steering wheel; a pool of blood on a street; a shot of a gurney wheel rolling. No story lines, just images, and not all of them recognizable, even.
Brakhage told the film seminar I was attending that as he was working on the second, he realized the third would have to be in the morgue. And that’s what The Act of Seeing with One’s Own Eyes is: 30 minutes of silent color images of autopsies. Except that where the first two films rarely if ever showed much beyond a closeup of a small detail of the film’s setting, and that often out of focus, TAOSWOOE showed clearly, and mostly in medium shots, the slitting open of abdomens, the peeling back of scalps, the sawing open of skulls, and the removal of brains and other organs. The real thing, not prosthetics, not dummies. Real bodies of once real people.
More than one person got up and left the theater crying. I was only about 20 at the time, but it was without doubt the most intense experience I’ve ever had in a movie theater, before or since.
I took the title as a challenge, as Brakhage saying, this is something that we all have to see for ourselves, that we all have to deal with death. It was only after the screening that he explained, in response to a question, that it’s the meaning of the word “autopsy,” auto=self; ops=seeing.; i.e. seeing for yourself what caused death.
It’s available on DVD with 25 other Brakhage films, although unfortunately, the first two parts of the trilogy aren’t included in the collection.