what are the rush hour times in tokyo?
Morning: (from where I live...)
Trains start at 4:30 AM and are packed from 5:30AM to 8:30AM. If you are going the opposite way, they are empty. (i.e. Pussen's train is empty coming from his apartment to our office since most everyone else is going the other way.) I live at a large station, so trains going into Central Tokyo are packed and the ones going the other way are empty.
Afternoon: (from our office area)
Most offices let out between 5:00-5:30 PM, Trains are packed for about 2 hours. But, it depends on what direction you are going. The trains going to the outskirts are packed until 8:00PM and then there is the last train rush around 11:30PM-12:30AM, packed ratio depends on where you are.
I tend to leave later in the morning and I can usually get a seat on the JR line or Subway. In the afternoon, I try to leave on-time and can manage to get a seat 50% of the time. (otherwise, you are standing of course.)
EDIT: After Pussen's post: Cabs in highly packed night areas are impossible to get. However, if you walk for about 10min, you can always get a cab somwhere in the middle. Cabs in my neighborhood are easy to come by all the time. Also, Cabs are you only option after all the trains stop (~1:00AM latest JR train), Cabs are also 20% more expensive after 10PM.