A couple of friends asked me for thoughts on finding great food in Japan. My observations may not apply to Hokkaidō, Tōhoku and Okinawa, which I did not visit yet.
The average food quality in Japan is quite high, be it Tokyo or one of the smaller towns and cities. The average sushi in Japan seemed superior to the best sushi I have had in Germany. The best sushi I had in Japan was also much cheaper than the ones in Germany. When key ingredients are sourced nearby, the prices drop.
Sit-down restaurants are not the only places you can find delicious food in Japan. Hole in the wall shops and food stalls (yatai) are great options. You can find rows of yatai in Fukuoka or stand-alone ones in different places. Some food stalls excel in one dish. Tamagoyaki (Japanese omelet) from a food-stall run by an elderly Japanese near Ōji station in Tokyo was my favourite.
Japanese restaurants specialise in specific genres of food. Prefer a sushi-only place or an Okonomiyaki place over one that offers many different kinds of food.
Long queues outside restaurants are common in all kinds of eating places, regardless of the price. Some of these lines extend multiple blocks and patrons seem happy to wait along roadside, under the sun for hours. If you have time, you can join them in the queue. If not, find a nearby place that offers the same kind of food. If one ramen place has a long queue, most nearby ramen places are likely to have equally good ramen around the same price range.
Best food options I found ranged from 900 to 1500 yen. But you will find cheaper and more expensive food that are delicious. One of the best ramen I had only cost 300 yen, while another cost upwards of 3000 yen.
Public transport can be your friend in Japan, but beware of fiendish train stations. Some train stations have more than 50 exits. If you have a destination to reach, knowing the closest train station may not enough. You need to know the closest exit as well. Else you will find yourself going around in circles. I found the train stations in Tokyo to have well marked-exits in English. This was not the case in many other places like Osaka station, which is a labyrinth.
So take the correct train (there are many train lines), get out at the correct train station, and take the correct exit. The chances of getting lost are still non-negligible. GPS may not help you in underground passages.
Train stations are themselves great places to eat. There are excellent variety on offer. But beware that the restaurants in major stations like Tokyo station are crowded and you might need to wait upwards of an hour to be seated.
If you find your way out of train stations, one approach to find great food is to choose a neighborhood with many options and then walk around. When you see something interesting, wait outside to be seated. Some places offer standing options. I find this approach better than hunting down a specific restaurant that is popular among food critics. If you really want to visit a specific restaurant, calling them to reserve a table is the best option.
Many restaurants are not visible from the streets. A narrow seven-storey building may have numerous restaurants, each specialising in a specific genre of food. So don’t just walk streets, also walk (or take the elevator) around some of these buildings. You will find many gems. Be mindful that you will encounter long queues of people inside these buildings, especially in Shinjuku.
Visit eating places at the times when the office-going Japanese has meals. Observe where they eat. Often these will be inexpensive places that offer delicious food. In such places, you might want to order food by pointing to what your neighbor is having. This is one way to try out new dishes.
In the evenings, small family-run restaurants offer an excellent environment, to eat and to socialise with locals. That’s an environment where the regulars can get rowdy but they are usually friendly. Most restaurants in Japan have a short table turnover time. People arrive, eat quickly, and then leave. Small family-run restaurants seemed to be a partial-exception to this. People hung around for an hour or two, drinking and chatting.
Various Japanese cities have their own specialty foods. If you don’t enjoy the food of one city, the next city may not be too far. If you don’t enjoy Hiroshima style Okonomiyaki, the next Shinkansen can get you from Hiroshima to Fukuoka in an hour, where you can try Hakata ramen or some less common dishes at one of the yatais.
Don’t forget bakeries, convenience stores and supermarkets. Baked goods are a delight. So are onigiri (rice balls) and cup noodles.
Mochi. Even the ones in supermarket tasted better than the ones I had outside Japan. Try variations such as daifuku (most commonly round mochi with red bean paste filling), yomogi mochi in Nara and warabi mochi in Kansai region.
Update on April 14, 2024: Edited paragraph as I have since visited Hokkaidō and Tōhoku.