If you're eating out in Tokyo, its important to be polite, especially in Japanese restaurants, where ritual is as important as the food. Take off your shoes at the door, and make sure that you thank the host as well as all the waiting staff as they serve you.
For an authentic Japanese meal, head for Takamura, which serves Kaiseki - The Japanese equivalent of Haute Cuisine, or for a slight western flavour, try out Nobu (now franchised across the world).
A really popular sushi bar that offers great value for money, is Heiroku Sushi where each dish costs around £0.75 and an Asahi beer to wash it down with goes for about £3.