One of the things I was most reticent about when coming to Japan was the Tokyo Metro. I’d heard of over crowding and people being pushed onto trains so that the doors can close. I have to say that I haven’t experienced anything like this although it can get very busy.
This is the train I get to work each day. This train is an express so it misses lots of stops and I can get door to door in 30 minutes.
People are a bit close together on the trains. In fact, on one train I saw a sign stating that people should sit close together (which they do). However, during rush-hour there are women only carriages as indicated on the platform.