I'm a visual person. And I need a map. Also, I can't just say map once without singing it to "Shots", thanks to a trip to Hawaii with a friend who was trying to hurry my map-getting-out speed. For the record, it did not help.
My Maps on Google is my favorite way to make custom maps.
I got a lot of the ideas on the map from internet searches and this awesome book called Make My Day by Lonely Planet. It's a neat way to build a day - choosing activities by morning, afternoon and evening. I am not sure we'll do it like that, but it helped us understand the best time to visit certain things.
Lonely Planet Make My Day Tokyo (Travel Guide)
Let's Get Lost in Japan! (and then find ourselves because of this super cool map ;)