This is a list of things/words you need to know:
Kinen-Seki and Kitsuen-Seki:
These will be the first thing your hear when you enter a restaurant. It means non-smoking and smoking. In Japan, smoking is still allowed in doors. This was a bit of a culture shock to me, since I grew up in San Francisco. We haven't had smoking sections since I was a child.
If you wand non-smoking you say "kinen-seki onegaishimasu".
Note: their little dividers will do little to block the smoke from wafting into your nostrils. Also, if you have sensitive eyes like I do...invest in some eyedrops...o_o
Oshibori(おしぼり or お絞り):
Wherever, you eat you will have a wet towelette to clean your hands. You will have this regardless of whether or not you will be eating with your hands.
Note: hot in the winter, cold in the summer
WARNING: DO NOT WIPE YOUR FACE WITH THIS (I've seen some salarymen do it. but it's a no-no)
Osusume(おすすめ or お勧め):
It means recommendation. Most places will have a recommendation written on the menu. So learn the kanji well...because you will be seeing it. Also, sometimes you won't be able to read the menu. It is very useful to ask your waitor/waitress what is their recommendation.
"Osusume ha.." is acceptable... or
"Anata no osusume ha nan desuka" if you are determined to speak in whole sentences.
LEARN THIS KANJI, IT WILL BE YOUR SAVIOR!
I love love...LOVE Teishoku! It is set meals! Considering that I was hungry for the first 4 months in Japan, I looked forward to these reasonably prices filling meals. Lunch time is of course cheaper, and it always comes with delicious miso(even at Denny's)
I find that the family owned hole-in-the-wall spots can be pretty darn delicious...so start looking! And share you favorite spots with your friends.
It means "to go". If you go to fast food restaurants they will ask you for here or to go.
Note: There are no such things as doggie bags in Japan. People will just look at you funny.
Whenever you eat at a restaurant you will almost always pay at the door. Before you pay, just say the magic words "betsu betsu" and they will very easily SPLIT THE CHECK. Each person will pay only for their own meal, and since gratuity is included it just makes it easier.
Note: I'm more impressed because I am American...Because if you ask an American waitor/waitress to split the check, they look at you as if you asked them to do advanced quantum physics.
"Gochisou sama deshita" (ごちそうさまでした):
"Thank you for a wonderful meal"
This is very useful for relationship building...and it's pretty standard for politeness.
Whether you live in a dorm or go to you favorite sushi place. You should say that as your are leaving. Say it loud and proudly, to further emphasize how delicious the meal was! It will make them happy, and make you happy for feeling like you are a part of the culture.
I had Kaiten-sushi(revolving sushi) way to often... so I used it regularly. The preparers will remember you, and it will help your cultural immersion in Japan!