I was in Osaka earlier in the week, and Kyoto after that. And these cities were also quite clean and orderly, with Osaka being the most orderly (and much more relaxed and slow paced, which makes order easier).
One of my favorite parts of Japan's cleanliness is their cars. They are all sparkling. Even the delivery trucks are shiny and splatter free! The gas/petrol station near me had at least two attendeds at each car, one to pump, and the other to clean the car's windows and paint!
Another fascinating thing is how escalators have two lanes, one for walking and one for standing. Why doesn't everyone so this?! It's so perfect!
Others in this thread don't speak too highly of Osaka, but it was definitely the most orderly and trash free of the three cities I've visited. Of course, these cities are quite huge, compared to cities in the US, so perhaps these conversations should be more fine grained, generalizing by prefecture rather than city.
I've found that I've been lining my things up neatly, and organizing my clothes and toiletries here in my in my hotel. It's been inspiring to see all the order here.