In Tsukiji market there are three stores on the same side, all with long queues in the morning. If you see them, just join any, you can't go wrong. I ended up spending $70 on breakfast there but it was worth it. I had never seen such a huge scallop in my life before. The Hong Kong guy next to me was totally amazed and ordered for himself too.
If you are in Tokyo, try Kyushu Jangara. They sell excellent ramen, but the thing is their menu is entirely in Japanese and waiting time is about 45 minutes. They have several branches all over, but the one I know of is in Akibahara. Just order "Zenbu Iri" for 980 yen, the meat will melt in your mouth. I swear.
Another place to look out for in Tokyo is Negishi. Again, menus are in full Japanese. There is one in Ikebukuro and another in Akiba, and a couple of other places. They offer grilled beef, pork, ox tongue etc. They serve rice cookde with barley and you pour a potato paste over with sauce to eat, very interesting. Also, the rice is free flow. Eat to your heart's delight. I managed four bowls once.
And in Kyoto, if you take the main road up to Kiyomizu Dera, look for a small alley on the left that leads to a small eatery. Order their Nishin soba, it is fantastic.
EDIT: I must add, bar the Kyoto place, be prepared to queue for the rest!