Fisherman's Lunch in Tsukiji
If you are looking for a cheap and delicious in Tokyo, I recommend going to the Tsukiji fish market. Tsukiji is famous for being the largest fish market in the world. You may visit it early in the morning to watch the fishermen negotiating the prices for tuna. When you are done with that, DO NOT FORGET ABOUT EATING THERE! At Tsukiji, there are numerous cheap but delicious, and extremely local restaurants catered for fisherman returning from a long night of fishing. Not only is anything related to fish good, there are also famous ramen and tamagoyaki places in Tsukiji. I recommend trying a fish donburi (bowl of rice with raw fish on top) and a ramen at one of the many stores. Prices will be around 1000 yen at lunch.
Tsukiji lunch is awesome!