I love stop motion animation. I was raised on the works of Oliver Postgate, and I love the Quay Brothers, so darkness in animation is not that new to me. It is such a versatile corner of the medium of animation and the tonal quality and feel of it, because of the variety of materials that might be used in it, is hugely variable too.
The first section with a family that moves into a house sponsored by a friend of their fathers creaks along, with the movie working perfectly to notch up the tension, while the slow disintegration of the family and the isolation of the children leads to the only kind of conclusion you could expect, pulling you along through the story with no friction at all.
The second section is the one that made me and my wife decide later that it had been a mistake for her to watch before sleep. A rat is flipping a house, there is a bugs problem. That is all I am going to tell you about the story. You get emotionally involved, it piques your interest intellectually, and it unsettles you the whole way through — the end unsettling you in the final coup de grace.
The third section still traffics in uncomfortable feelings, but it is not as visceral as either of the previous movies. Its sensibility is in keeping with the other two sections, but it is definitely a less difficult story to process.
I would definitely recommend it, but if you are sensitive to these kind of things, give yourself a little space between watching it and trying to sleep.