Serious Eats - seriouseats.com

Ok take a deep breath... this is going to be super long.

I'm SOOOO jealous that you are going to Japan this time of year!! best time to be there as a food lover.
First of all, its the right season to eat new crop of rice. New crops of Koshi-hikari and Akita-komachi are just so good that you only need something salty (like good Japanese pickles) to eat a big bowl of rice.

Vegetables and fruits:
Kabocha squash
Eggplants
Japanese sweet potatoes (Ishiyaki imo (sweet potatoes slowly roasted in hot pebbles) are the best. You need to find a cart with singing ad)
Mushrooms: shiitake, maitake, shimeji (I don't think Matsutake is worth the money anymore)
Chestnuts (if you like sweets, you MUST try some chestnut sweets. Western and Japanese. "Mont-blanc" at a cake shop means cakes with chestnut cream)
Ginko nut (don't worry, the stinky flesh is washed away... they are so tasty in Chawan mushi)
Kyoho grapes. people PEEL grape skins. it's a normal practice in Japan. they are not seedless, so be careful.
Asian pears. "20th century pear" from Tottori prefecture is widely available, but my personal fav is Kaga pear. they are ginormous.
Fuyu persimmon.

Fish:
Sanma (Pacific saury). a whole fish requires a bit of chopstick skills (though it's the best!), but you can get sashimi and sushi during peak season. yuuuuum.
Mackerel. if you like fish.. miso-ni (simmered in miso broth) is the best.
Salmon

Now, I don't know much about Nagoya, but they have some nationally famous foods. Miso-katsu is one (deep-fried pork cutlet with miso sauce). Nagoya kohchin, a variety of chicken that is from there is also tasty.
While you are in Kansai (Osaka & Nishinomiya), don't forget to eat udon and okonomiyaki. In these two categories Kanto loses (I'm from Kanto area). Osaka (Dohtonbori) is known for "kuidaore" (eat till you drop). Lots of good street food there!

Tokyo- depends where you are going. If you are into sushi, don't miss Tsukiji (but good places are only open until they run out of fish, usually around 1pm). Midori sushi is also great, and there's one in Shibuya. But those famous places requires waiting..
If you like soba you should at least go to a place where they make their own noodles.Yabusoba in Kanda comes to mind but there are so many "teuchi-soba" (means homemade soba) places.
Izakaya is a great place to eat many interesting dishes as they come in small portions. Look for red lanterns at night! Yakitori places are a bit similar to Izakaya and I loooove yakitori, but chances are you'll encounter chicken innards, just so you know.

For both Tokyo and Yokohama, check out bakeries (and cake shops). You'll find interesting breads, both sweet and savory, and fantastic cakes.

Yokohama- It may sound silly but there is a big Chinatown. In this season they may already have the steamed chinese buns out... they are huge and tasty! There is also the Ramen museum (actually in Shin-Yokohama, not Yokohama). It's a port city, which became famous for their Western-influenced foods (it's the first place to sell ice cream- and beef dishes). As a consequence there are many Yoshoku (Western-Japanese fusion from Meiji era) restaurants in Noge. Typical yoshoku menu include omu-rice (chicken rice wrapped in omelet), hayashi-rice (sort of like beef stroganoff, but demi glace-based), hambaagu (pan-fried meat loaf patties), panko-crusted fried shrimp, etc. Otherwise there are tons of trendy restaurants people go on a date. It's a popular date destination

I can go on and on, but I'll stop here. let me know if you want to know something in particular!

ten-ichi in ginza (they have other locations as well) - was recommended by my guidebook - best tempura i've ever had.

While neither a meal nor off-the-beaten track, if you happen to be visiting Sensoji (the main temple in Asakusa in Tokyo), make sure to get some agemanju (sort of like a deep fried sweet dumpling). The best ones are from a stall right before the entrance to the temple on the right hand side. They'll probably have kabocha agemanju since it's seasonal.

Do not miss the ginko nuts. It's also oyster and ikura season (salmon roe). Also, sweet potato ice cream, which is best in Kamakura but you can get at the Sensoji Temple. In Harajuku, you can make your own Okonomiyaki at Sakura-Tai. Vendors should start selling roasted sweet potatoes on the street soon. They put them in paper cones, like a vegie ice cream cone. No wonder people here are so skinny. Good luck and let us know how it goes.

Go here - http://accidentalepicurean.com/2009/07/abalone-tuna-jaw-conch-and-more-charcoal-grill-in-tokyo-japan-wvideo/

If you can find it it's one of the best meals I've eaten. Also just click the Japan or Tokyo tag once there to see other places I enjoyed. I haven't put up Xex Omae yet (formerly Xex Morimoto). Really amazing meal there as well.

Paul

MOS Burger!!! I was meaning to try the more unusual variety (e.g. eel, rice burger, teriyaki, etc.) but I was always too weak to resist spicy MOS cheeseburger.

hmw0029's list is very good, and I would like to add:
- tenmusu (shrimp tempura rice ball) in Nagoya
- Curry Museum in Shin-Yokohama
- hiyoko manju (white sweet bean paste wrapped in a thin layer of... pastry?) at various train stations in Tokyo - good for souvenirs too http://www.hiyoko.co.jp/shohin/hiyoko.html
- conbinis (convenience stores) and department store food sections