Because there are so many chain restaurants in Japan, you probably need / have to eat there from time to time.
Here is a selection of the best ones... Please share your own discoveries in this thread.
Tengu (天狗, Izakaya)
Tengu is a chain of cheap izakaya. Still, in the range of 2000-3000 yens per person (with drinks), it is probably your best choice! They have many izakaya in Tokyo, usually located very close to the train stations. There is a large selection on the menu, which is printed with pictures of the dishes, and some seasonal selection. They have a good selection of sashimi, sushi and californian sushi, of course, but also grilled meat or even pizza with Parma ham for around 600 yens! Nihon-shu are good, too, although there are not so much to choose from. Popular among businessmen, the place is usually noisy, especially in the largest rooms. There are however also smaller alcoves available, which are great for small groups.
Web : www.teng.co.jp/tenpo/shunsen/index.shtml
Links with all branches in Japan : www.mapion.co.jp/custom/teng/index.html
Tsunahachi (つな八, Tempura)
Tsunahachi is a famous tempura chain restaurant with about 20 branches in Tokyo, especially around Shinjuku station. They serve mostly teishoku, sets comprising of course tempura, rice and for most of them sashimi. The food is really tasty - tempura are cooked and serve immediately, which means that often food is arriving in sccessive waves - and the price low, as sets start from 1600 yens; more expensive sets are however recommended...
For years, I used to bring friends from oversea there on their first evening in town, and all were always delighted. Furthermore, all restaurants have food displayed outside, which obviously is a plus for people who are not used to Japanese food.
I would recommend the branch in the Takashimaya building in Shinjuku (near JR new south-east exit), on the 13th floor. Although there is often some waiting time, it is easy to locate.
Web : www.tunahachi.co.jp
Links with all branches in Japan : www.tunahachi.co.jp/storelist.html
Onyasai (温野菜, Shabu shabu and sukiyaki)
With more than 62 branches in Tokyo - and much more around the country - you will easily find this popular chain restaurant specilized in shabu shabu (type of Chinese fondue) and sukiyaki. Popular for parties, as there are many nomihodai and tabehodai sets, it is also a nice place to enjoy lots of meat! You can choose two types of flavor for the broth, and just poor in it the meat you order. The prices are really low (count 2000-3000 yens with a drink), and although you don't get premium meat, it is a nice place to get filled, especially in winter.
Check their web page for a 500 yens discount ticket sometimes available!
Web : www.onyasai.com
Links with all branches in Tokyo : www.onyasai.com/cgi-bin/shp/shopsearch.cgi?word=tokyo
Gansoyushi (元祖寿司, Sushi bar)
20 branches in Tokyo. I usually go to the one in Kagurazaka, 300 meters from exit 2B or 3B in Iidabashi (sushi bar on the left side of the road, with a characteristic clear wooden facade). A very fine kaiten sushi chain, with a couple of great specialities like tempura sushi (shrimp, asparagus, etc). Those are just excellent and very original. Also a cheap place, count on 1500 yens.
Chaîne de sushi bars avec une vingtaine de succursale sur Tokyo. Je vais en générale à celle d'Iidabashi: à partir de cette station, sortie Kagurazaka (2B ou 3B), monter la rue sur environ 300 metres. Le sushi-bar est sur la gauche, avec une facade recouverte en bois clair.
A mon sens, le meilleur sushi-bar (kaiten sushi) que je connaisse. Produits tres varies, tres frais, les cuisiniers au milieu preparent tous les sushis que vous desirez devant vous, ou vous pouvez vous servir sur le tapis roulant usuel. Quelques specialites, comme les tempura sur sushi (asperge, crevette, etc) - delicieux! Tres bon marche, compter 1500 yens.
Web : www.gansozushi.com
Links with all branches in Tokyo : www.gansozushi.com/home.html
Chaochao (餃々, Gyoza)
Always very small (usually 10-15 seats at a counter and sometimes 2-3 tables), those shops offer a fantastic selection of gyoza, with a special emphasis on unusual combinaisons: cheese gyoza, okonomiaki gyoka, spanish pork gyoza, ... There are almost only gyoza offered on the menu, but all are really excellent, and the prices are low: 300-400 yens for 5 gyoza. Also, a huge selection of good quality sake cups (nihon-shu stored and served directly in a glass). Strongly recommended.
Ces restaurants sont toujours très petits, construits autour d'un long comptoir avec parfois quelques tables. Leur spécialité sont les gzoya, avec un intérêt particulier pour des combinaisons plutôt inhabituelles, telles que des gyoza au fromage ou aux okonomiyaki... Le menu ne comporte pratiquement que des gyoza, mais tous valent la peine d'être essayés. En particulier au vu du prix, 300-400 yens pour 5 gyoza. En plus, de nombreux sake cup sont disponibles: il s'agit de nihon-shu stockes et servis directement dans des verres, qui s'ils sont parfois de basse qualité, sont vraiment très bons dans cette chaîne. Chaudement recommandé.
Web : www.gyozaya.com
list of the 11 restaurants in Tokyo : www.gyozaya.com/shop_chiiki/tokyo/index.html