We took the bullet train to Kyoto. Went to a bento emporium in Tokyo Station called Ekibenya Matsuri. Had probably 50 different types to choose from. They even had one with a pull tab that heats up your food!
We stopped by the Ghibli Museum in Mitaka outside of Tokyo. It's an awesome spot for fans of their movies. Unfortunately no photos allowed inside. In their cafe they even have their own beer!
Afterwards we hit an izakaya in Tokyo. Very big city feel to it so not an intimate place (it was huge with tons of corridors and private rooms) but still authentic. Lots of salary men and office ladies drinking, eating and smoking.