As I sat at home in New York chomping on my New Year's foie gras, I never thought I'd be making a post like this so soon.
Basic Food & Drink Tips in Tokyo.
Don't eat convenience store food or KFC, McD's, MosBurger etc, more than once. It's crap. No matter where in the world you go, a plastic wrapped sandwiched with the crust cup off and pre-packaged microwaved burrito/hot dog/gyudon is not what you want to be eating. Would you do that at home? Then don't do it here. There's a universe of great cooking in Japan no matter whare you are.
Stay out of chain resturants, whether they be Japanese or international chains. They suck in your country and they suck here. You didnt come to Japan to have dinner at Outback for fucks sake. Don't worry about the menu or anything, resturants are businesses and they want customers because they enjoy ...what's that thing that businesses do.... oh yeah making money. Most places won't care if you come in and are clumsy with the menu (as long as they're not being slammed with a huge crowd at the time). Learning Kana, Katakana, (and the numbers 1-10 in kanji helps though. If you're not retarded, it should take you a week of 1-2 hours of study per day to nail it down to almost second nature). There is one exception: in Shinjuku, there is a Krispy Kream. It is awesome.
Many but not all resturants close in the middle of the day between lunch and dinner. This is less true in tourist heavy areas, but then again tourist heavy areas tend to have crappy tourist traps that overcharge you for a plate of sushi or bowl of udon with lemongrass in it. Plan for this, it's worth the wait.
Look for uniforms. No, not on the staff, on the customers. Real food is only eaten by real people, and nothing says real people in Japan more than a uniform. Postal, Utility co, Construction, it doesn't matter. If there are uniforms at the tables, the food is gonna be good.
Izakaya. Americans; ever go to a run of the mill diner and know what you want to order before you even see a menu? That's because most diners serve faire so similar, that it's almost a universally known menu to most people who know them. In Japan, this is the Izakaya. With a few reional specialties, most of these places have the same type of menu. You can be confident that even if you can't read a word of the offerings, that if you know the basics and know what you want, they'll bring it to you. If you live in/near New York City, there are a few Izakaya type places that you can practice this with (one of the more popular being called "Kenka" on St. Mark's place). Keep in mind that much like with diners and lunch counters, people don't go to these dives for the "ambeeaance."
Vocabulary. Learn these words: Muryou; Free. Tabe Hou-dai; all you can eat. Nomi Hou-dai; all you can drink (yes they mean booze, though you usually need a group of 4-5 or more), Margarita: ok, don't go into a place looking for a Margarita, because they'll probably end up bringing you a Margarita, so if you want a Margarita and not a Margarita, make sure you specify that you want a Margarita and not a Margarita.
Beer; Although beer out of a vending machine is a wacky novelty to just about everyone else in the world, only to this once if you have to just for the sake of doing it. Vending machine beer is going to taste exactly how you think it is going to (that's Stella-skunky by the way). And the machines are almost gone now too, the only ones that exist are now in private buildings which have limitations on who can enter. Also Japanese beer only recently figured out that there are actualy types of beer out there other than pilsner/light lager (aka McBeer). There are actually some interesting dark porters coming out of Yebisu right now, and most resturants have embraced the American Black&Tan which is a layered pint of half Stout and half Light Lager (or Pale Ale), which in Japan is called a "Half & Half." (FYI don't ever order this drink in Ireland or you're likely to get punched in the face, since Black & Tan means something totaly different there). So for beer in Japan, expect the German style to proliferate, and only drink where they have "nama" which means draught. Also, don't think you can guage Japanese beer from outside Japan, since it is brewed locally wherever you are (for example, in the USA Kirin is made in California and upstate New York, Sapporo is made in Ontario Canada, and Asahi is also made domestically except for those half liter cans). Finally, in Tokyo the concept of a "pint" is nonexistand, but in Osaka it's standard (I told you Osaka was better). If I lost you at "pilsner" then you're not a beer drinker anyway.
Wine; With apoliogies to the French and Itaians, this is very much a luxury item. Many establishments which offer wine (there are a lot in Tokyo) much like the USA offer it by the glass, for what seems like a very good price. However that's actually bullshit. When I ordered a glass of Dolcetto D'Alba for what I thought was a good price of 600 yen, I was more than a bit dissapointed when I was brought a massive Bordeaux glass with about 2.5 ounces of wine in it (that's just a tiny bit more than amount you'd pour for a simple free tasting). This concept was hammered in whin I went to the basement of the local department store where they sell the sake, and saw a bottle of Sutter Home cabernet from 2005 selling for 35,000 yen (that's over $35). Even the Australian lables aren't as cheap here as they are in the U.S., and don't even ask how much the Chateu Nuf de Pap was selling for. If I lost you at Dolcetto D'Alba, then you're not a wine drinker ainyway.
Sake; Called Nihon-shuu, it has unfortunately fell a bit out of favor with it's own domestic market. This is the best bang for the buck in these parts. Unlike the paint stripper known as Sho-chu, Japanese sake is very mellow and has as much of a spectrum as Europien stye beer or wine. There are full bodied dry ones that could almost be described as tannic (Dai Ginjou), there are fragrent fruity ones which go well with almost anything from sushi to icecream. There are dessert sakes, bitter sakes, and seasonal sakes. There are even aged sakes (which may not really be a great idea, but hey... whatever). Things like terroir and climate play a heavy role in the final product. Add to that the fact that about half a gallon costs about US $20, and it's mana from heaven. If I lost you at Dai Ginjou, then get out there and learn you some about this art form. A good and reasonable priced U.S. Domestic brand is called Momokawa (Peach River) from Oregon. For imports, look to Tenzan, Akita Homare, and NamaHage (mention Shirayuki, Gekkeikan, or Kurosawa, in my presence and I will punch you in the face).