That is really a difficult question... If you spend lots of budgets, you can have seriously nice meals but I will list a so-so budget list which most people can probably afford. I also chose from places that are close to major sightseeing areas.
1. Sushi: Nemuro Hanamaru (Tokyo Station)
It's a conveyor belt sushi restaurant in the shopping mall KITTE near Tokyo Station. There are numerous conveyor belt sushi restaurants in Tokyo but this place serves really good sushi considering the price. They are originally from Hokkaido, which is said to be the source of great seafood. You will be able to taste the real sushi and experience the fun of conveyor belt sushi here.
2. Tempura: Dote No Iseya (Minowa - near Ueno)
They are a Tendon (tempura rice bowl) specialized store. I have never eaten tempura (tendon) more delicious than here. Although their pieces come huge and have quite strong taste with thick flavored sauce, my stomach did not feel heavy at all. I can understand they are operating for 128 years! The building is very old and atmosphere is great as well.
3. Tonkatsu: Marugo (Akihabara)
Tonkatsu is deep fried pork cutlet. There are numerous tonkatsu restaurants in Tokyo but Marugo's tonkatsu is totally different. It's thick, juicy pork with crunchy dough is the only one. The best partner of white rice.
All of the places have quite long queues all the time. So visit them when you have plenty of time!