Still in Japan? Highlights from my trip 4 years ago:
1) convenience store breakfast. nigiri from 7-11 are great. Just make sure you open the package correctly
2) Shaka-Shaka Chicken from McDonalds
3) "fast food" So it's not fast food exactly, but simple sit down meals. Curry, ramen, udon. Stuff that's typically a little more fancy in America, but you can eat there for relatively cheap and I thought was really good.
4) Okonomiyaki/moncha. In Tokyo, there's a neighborhood that my native friends took us to with shops and up and down the street. They chose one based on a recommendation out of a magazine or guidebook.
5) Cheap sushi. We went to a Kaiten Sushi place in Kyoto. Wasn't the best I had, but at 105Yen/plate, fresh is all I really need. As an added touch for cuteness/ambiance, when you order items instead of picking them up off the belt, it comes to you automatically pulled by a mini bullet train.
6)
http://wikimapia.org/12593255/Nippara-Limestone-Caves Was a good half day to visit. ?90? minute train ride each way, and then a bus, then a bit of a hike.