<font face="Verdana, Arial, Helvetica, sans-serif" size="2">The N'Ex (Narita Express) is reservation-only so you're guaranteed a seat.</font>
JR also sells a limited number of standing-room tickets on sold-out NEX trains which, IIRC, force the buyer to stand at the end of a specific carriage (cannot stand in seating area or in another carriage).
As far as commuter trains go, they are manageable except:
- between 7 and 9am inbound
- between 5:45pm and 7pm outbound
- last outbound trains after 11:30pm (the worst, as many of the passengers are drunk)
For the subway and Yamanote line, there is no real inbound/outbound; they are crowded at similar times.
Crowded means up to 400 people squeezed into a car designed for 150. Large station attendants with white gloves do help pack in at some stations
If you have to take a train at those times, you should:
- not have any bags
- know where your destination station is, and inch towards the door 2 stations before; there usually is a bilingual route map at least above the two end doors
- know which side to get off (sometimes indicated on map or LED)
- stand where you can brace yourself. I go for a wide stance with my feet forming a line 45 deg. from the axis of the train. JR trains have slower acceleration and wider turns (no hands ok), some private lines with older rolling stock are much bumpier (no hands very difficult)
- keep your hands up in order not to be accused of groping
- in the summer, you'll sweat. Locate AC exhausts and stand under them, unless you care more about your hairdo. In my experience, Keikyu has the best AC, followed by JR, subways, and last, Tokyu lines, which turn off AC before the last station to save electricity

- try to avoid being behind a shorter man with greasy hair, it can make trips quite unpleasant
The next steps in the fine art of Tokyo commuting include:
- knowing which carriage and door will be exactly in front of your exit stairs; all trains stop at the exact same position
- choosing an unpowered carriage to minimize exposure to magnetic fields
- learning how to take a nap while standing, and magically waking up right before your station
- moving to a place from which you can commute against the flow
As a westerner, you'll be given a little more room than locals.