30 useful tips for travel in Japan

The Flow of the Japanese Restaurant, and the Japanese to Use
Conversation
Meal-ticket vending machines and self-serve aside, you will inevitably find yourself in a situation where you must communicate with restaurant staff. Even with language difficulties however, it's very easy to have a smooth experience at a restaurant in Japan. With these core tips for language and manners, you're almost guaranteed to leave the restaurant feeling satisfied, and avoid any uncomfortable misunderstandings.
Restaurant flow
Let's follow the typical restaurant flow, from being seated, to ordering, to paying.
You will be greeted by a restaurant employee and they will generally ask how many people are in your group:
1 person - Hitori
2 people - Futari
3+ people - Number + 'nin(people)', (san(3)-nin, yo(4)-nin, go(5)-nin, etc...)

Next, if the restaurant has a smoking section, they will ask "Smoking (Kitsuen)", or "Non-Smoking (Kin-en)". Indicate if you prefer Kitsuen or Kin-en to this person.

Once you are at a table, ask for an "English Menu (Eigo-no-menu)" if you wish, or simply begin to browse the menu available. Many places have the name of the dish written in the English alphabet, or pictures as well. The server will likely not ask you right away for anything, but they may inquire about "drinks (Nomi-mono)". You can order a drink off the menu by pointing and saying "This (Ko-re)". If you would like more time, say "Not yet (Mada)".
Ordering
What will likely happen, is your server will seat you, bring glasses of water, and leave. The reason for this is that they are waiting for you to signal them when you are ready. Some places will have a call button on the table, but you can always signal them with your hands and say "Excuse me (Sumimasen)". This is not rude, but is actually expected once you have made your decision from the menu.

Any time you need something, signal the server with "Sumimasen", and point to the menu using "Ko-re". If you want more than one of a particular item:
Ko-re + ( number of items)
1 item – Hitotsu ex: Ko-re hitotsu (one of this)
2 items - Futatsu
3 items - Mitsu
Do not hesitate to use "Kore" in combination with point or numbering with your fingers.
Paying
After you have finished your meal and wish to pay, ask for the "Check (Kai-kei)". In general, they will bring you a piece of paper with the price written on it. Take it to the register and pay, or pay at the table if permitted. Many of the more commercial places will take credit card, but for smaller restaurants, particularly outside of city centers, cash will be the only option.Please be sure to carry plenty of yen at all times.
Helpful phrases and words to use with your server:
Sumimasen - Excuse me
Arigato - Thank you

(item) o kudasai - (item) please
o-mizu - water
o-hashi - chopsticks
o-sara - plate
tori-zara - small plate
Mizu o kudasai - Water please
Mizu o futatsu kudasai - Two waters please
Torizara o kudasai - A small plate please (for sharing perhaps)
Gochiso-sama desu - Thank you for the meal (not totally necessary, but is a nice way to thank the staff/chef)
These are some of the basic phrases that can be used in almost any sit-down restaurant during your travels in order to get what you need. Remember, people are glad to have you in their shop, and speaking very slowly and clearly with body language will always be indispensable for communication.