I have had my share of being groped or at least rubbed provocatively by Japanese men on trains. Some of it, of course, is completely accidental. However, there were times when it definitely was not so innocent or at least was mutually
Another, I was on the Keio line leaving Shinjuku at night and it was very crowded. A young guy seemed to not only welcome having me pressed up against him, but he turned himself so that our crotches would be pressed together. This wasn't actually either of us groping, but the force of the bodies and the movement of the train keep us both aroused as we were smashed together at the groin.
There is an urban myth among gays in Tokyo that men who are seeking mutual accidental encounters (rubbing, groping or even stealthful mutual masturbation) will congregate in the last car (or is the first car). Once I saw a tall foreign guy in overalls apparently getting a hand job from a shorter Japanese man in the last car on the Chuo (Orange) train.
Finally, there used to be a wild event on or near Halloween (Oct 31) weekend on the Yamanote train (green circle line around central Tokyo).
in a lot of cops to stand guard around Halloween weekend. Also the number of party animals has dwindled since Japan has undergone quite a long economic recession - there are just not a lot of young party-going foreigners around since good jobs are harder to get these days.
Still I have no doubt the train-groping will continue to go on. It's just too tempting and almost impossible to avoid really since so many people are crammed into a small space. Fortunately, it mainly only unbearably crowded in the rush hour morning commute. The leisurely mutual brush-up-against-you teases are still likely to occur on the afternoon and evenings.