The only examples that come to mind are some of the more depressing movies that are just hard to watch like *Grave of the Fireflies* or *Schindler's List*, but those don't quite feel like a fit. They good and I don't want to watch them ever again but that doesn't make them bad.
In my mind it has to be more along the lines of an arthouse film that is so artistically pure that it's unwatchable or a film that is technically brilliant but the concept is fatally flawed, like they succeeded in making the bad movie they wanted. Almost like what *The Producers* were trying to do.