It’s true how I’ve followed a number of rules in eating Japanese food, since I almost always eat Japanese food when I’m out with anyone, or even just by myself. Some of these I learned online, while most I learned from my Japanese friends and my personal experience in Japan.
It’s not just in a restaurant, but in Japanese dining in general:
Not really a rule, but it’s been a habit for me whenever I eat at a Japanese restaurant (sometimes, even non-Japanese ones, heh). Itadakimasu right before eating, after I say a short prayer; and Gochisousama deshita after my meal.
First, in using chopsticks, especially the wooden ones, do not rub them together before using them. You might do it just to remove a splinter or something, but it’s disconcerting, and is actually rude for the people working there. It sends a message that you think the chopsticks they use are subpar.
Second, Always use the other end of the chopstick that has not been in your mouth to pick up food from communal dishes. And don’t pass food between chopsticks. Also, don’t use them in reaching your food from the other end of the table. That’s rather impolite. I had a personal experience with this, and while your Japanese friends may not say sit out loud, they’ll notice.
Third, never leave the chopsticks sticking straight up in your food. This one’s a general rule, though some people still don’t get why - it’s because it symbolizes death/funeral and you wouldn’t really want death anywhere near your dining experience. Just rest them on the edge or something.
Before, in eating sushi, I used to dip both the topping and the rice in wasabi sauce. However, in eating sushi the right way, with the chopsticks, you just dip the topping to the wasabi sauce, and not the rice, since you still want to taste the flavor of whatever topping you have and not taste wasabi altogether.
The ginger which is usually served with the sushi set is supposed to eaten every time you try another kind of sushi, to neutralize the flavor in the tongue. I don’t like ginger though, so I avoid that as much as possible.
Also, eating sushi with the hands is completely acceptable. I do that sometimes, but most often, I still use chopsticks.
For noodles, especially hot ramen and udon, the restaurants I go to usually recommend to eat them as soon as they are served, and for a good number of minutes only - maybe 10 minutes if you can - to truly experience the taste. Back in Japan, slurpring is actually encouraged, just so the customer can let the chef know that they enjoy the noodles. Slurping in the Philippines is not as encouraged, culture-wise, but with the recent ramen craze, I’m pretty sure they wouldn’t mind.
Okay, this one’s not really an ~etiquette~ more of a habit, again. I always remember to order tea, hot or cold, more often rice or green tea, rather than water. I’m a tea person, and I feel like a Japanese meal wouldn’t be complete without it.
Then there are tips. In Japan, tips are a no-no. But in Japanese restaurants here, who wouldn’t say no to tips? They even have service charge… Heh.
There you go, hope that answers your question!