There are ways and there are ways. Here's a short and dirty guide to steering your way through the cultural mores of Japan's restaurant scene.
You might want to check my previous pieces on Japanese culture, its obsession with rice, a short history of sushi, Sushi in the Land of Samba and a recipe for Fox Noodles.
What to Wear: Most diners are casually dressed, whether going to a cheap or expensive place. Look nice and presentable.
The Shoe Issue: Restaurants that have tatami rooms will ask you to remove your shoes before entering. When heading to the washroom, you are expected to use special bathroom slippers. LEAVE THE SLIPPERS IN THE BATHROOM and do not wear them upon your return.
Ordering: The best thing is to ask for the chef's choice (omakase), which is how most people eat.
How To Eat: Sometimes, a meal comes that has several "pieces" and you may not be sure exactly how it's to be eaten. Feel free to ask the wait staff whether you should combine or stir things. Drink the miso soup as if it was in a cup and pick out the big pieces with your chopstick. It is customary to finish your meal down to the last grain of rice. Do not burp.
Table Talk: You must refrain from unpleasant conversation - anything that would approach issues of the toilet or anything unappetizing. Oh yes, never blow your nose at the table.
Sushi: You can use fingers or chopsticks. If the sushi is meant to be dipped in sauce, only dip the fish part – not the rice. Eat the sushi in one bite. You can even ask the chef to cut pieces in half if they seem too large. By the way, you should not be adding wasabi to your soy sauce. If eating gunkan sushi (think of roe bits nestled in a seaweed cup), you should pour the soy over it.
Sake and Beer: Never pour your own, it's the responsibility of your companions and naturally, you must do the same for them. Do not start drinking until everyone is served. A drinking salute is usually "kampai."
The Finish: You'll be given a towel. Wipe your hands ONLY, fold it neatly and place to the side. Use it to dab your fingers during the meal.
Tipping: Service is included on the bill.
Words to Remember: "Oishii" (delicious) or better, "gochisosama (deshita)" (Thank you for the meal).
PS: Awhile back, I did a little piece on Asian table manners in which I noted that in Japan, one should NEVER stick chopsticks into rice, standing up, as that is something done at funerals.
If you are further intrigued by the intricacies of etiquette, take a gander at the tea ceremony.