AND while we're on the subject of creepy commuter trains, what's up with those, anyway? I was just thinking about it, and I can't remember any anime with anything good that happens on a commuter train.
In Boogiepop Phantom, a commuter train gets invaded by some sort of supernatural thingy that travels as electricity. Think of those sinister scenes in commuter trains in Lain, or the murders in Tokyo Babylon, or the dark thoughts going through Mima's head in Perfect Blue, or Shinji's anomie in episode 4 or Evangelion, or those weird surreal interior dialog scenes in commuter trains in the later Eva episodes. Even in Oniisama E, commuter trains are associated with Nanako's anxiety, or some other active problem. Even dead children travel by commuter train, in Grave of the Fireflies.
Yes, I'm aware of the sexual assault problem on Japanese commuter trains, and I can see why women would find them vaguely threatening, but even to males like Shinji or Seita they seem to be associated with bad things happening.