In a morning train bound to Shinjuku, or Shibuya Station !

I would definitely recommend you to try taking morning trains which are destined to Shinjuku, or Shibuya station to arrive in between 8:30AM to 9:00AM, at which most of Japanese companies start working, then staffs and employees are most likely to take ones around this time to be able to be at office in time . I guess it's better (meaning worse in terms of how jammed!) for you to pick cars located in the middle of a train; probably in the car #4, or #5 when a train consist of 10 cars if you want to experience real one!

When I'm asked to name top 3 notoriously jammed, packed, and "squeezed-as-the-heck" lines in Tokyo in the morning, they will be: 1) Saikyo line (southbound from Saitama to Shinjuku), 2) Odakyu line (eastbound from Odawara to Shinjuku), and 3) Tokyu Den-en toshi line (eastbound from Kanagawa to Shibuya).

One thing to keep in mind, especially when you're a male passenger, is that you should be very much careful about possible behaviors, postures, or positions of your legs and arms that could be harassment in a jammed train so you would never ever be treated as a criminal by it even though you never intend to do so.