Been living in Japan for 7 years and there's not much that bothers me apart from the morning train...
A train is said to be at 100% capacity ( Josha ritsu 100% (乗車率100%) じょうしゃりつ) when all seats are taken and all standing space is also filled up with everybody standing shoulder to shoulder. The train I get on in the morning is probably about 150 - 200% capacity where you can step on somebodys foot by accident and keep your foot there without anybody complaining. This is because its sooo packed that you cant even adjust your footing. I suppose this is not as bad as the tube back in London where you have to kind of bend your neck sideways if you are standing next to the door as the shape of the train is round - get squashed and risk doing permanent damage to the neck.