Bamiyan is a Chinese-style restaurant with plenty of locations across Tokyo. For about ¥1,000 you can have a good-sized set meal of noodles, stir-fries, dumplings, etc. Many people order a main dish with some gyoza (dumplings) as a side order to share. Some locations also have an all-you-can-eat shabu shabu (hot pot in which you dip various ingredients) that is so worth the try! They offer many kinds of meats and vegetables and also they have a dessert serving at the end. The shabu shabu courses are over ¥1,700 per adult, ¥999 for elementary school children, ¥499 for toddlers and ¥1,299 for people over 65. Granted that latter option is over ¥1,000 but still reasonable for the price!
Saizeriya serves Japanese Italian cuisine at a super reasonable price. Most dishes are between ¥400 to ¥800. They have pizza, pasta, curry, salads, Hamburg steaks, Doria, and plenty of desserts too. These are all staples in Japan, and Saizeriya makes them pretty darn well for the price! The Doria at a mere ¥399 is quite surprising! For reliably good Italian/Japanese cuisine that won't break the bank, many families in Japan go to Saizeriya.
Cafe Restaurant Gusto
Cafe Restaurant Gusto is one of the best places in town for some seriously cheap and delicious Hamburg steak! They come served on a piping hot iron plate and they have all kinds of toppings and sauces to have them with. They even have some with cheese fillings if you have an appetite and want to pack some calories! Also, they have some surprisingly fancy dessert pancakes that you might want to try if you have a sweet tooth. The prices here too are for the most part below ¥1000.
Remember this place if you want a laid back, cheap, breakfast buffet! They serve here a mix of Japanese and Western foods. You'll find both savoury and sweet items on the menu. You can have miso soup, rice, wiener sausages, pancakes, waffles, fruits vegetables, and coffee jelly! The price is ¥680 on weekdays and ¥780 on weekends from 7 to 10:30 AM. Go there for lunch or dinner and you'll also find plenty of cheap satisfying dishes.
Denny's is originally an American chain, but it is highly popular in Japan, with 29 branches in Tokyo alone.
The menu is totally different from the one in the U.S. You can try Japanese dishes such as tempura and tonkatsu (pork cutlet) at Denny's Japan! They also have western style dishes and desserts. The parfaits they serve are inspired by the ones you would find at fancy fruit parlours in Tokyo, but they're only a fraction of the price. Denny's Japan is a good place to just have dessert and coffee too!