When you need a waiter/waitress or bartender in Japan you can yell 「すみません」(“sumimasen”/excuse me) from wherever you may be seated. This is a perfectly acceptable thing to do. Someone shall immediately flash over to help you, regardless if they were at the table next to you or on the opposite side of the hall.

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In most countries in the West, tipping someone for the service they have done is very common, and typically a social must—whether people want to or not. There is no such custom of tipping in Japan. Rather so, tipping is considered demeaning.
It may be confusing at first for foreigners when they arrive in Japan, however, once you become accustomed to this you may find it refreshing. The politics of tipping can be stressful for customer and host alike. Without tipping in the equation the service environment is more relaxed. So, when in the nation, remember not to leave some extra change for your driver or waitress—they will most likely run after you to return it instead.

In the West, most people, especially men, will more likely than not hold open a door for someone if they are close behind or in front of them—that is not to say that it is very common nowadays in the West as well. This is not as common in Japan. The Japanese are less inclined to hold doors for a stranger, for there is no real culture for it. That doesn’t mean that the Japanese lack chivalry. It is simply not a common practice that is taught to people. It does happen sometimes, however, do not feel offended if no one does so for you and do not feel that you must do so yourself.
I am quite lucky actually, for most people have held doors open for me if I am right behind them or am walking out the door and they are going in/vice versa. Haha. 😛

The Japanese tend to avoid conflict; they try not to deliver bad or even sad news directly. Criticism is usually softened in Japanese — you need to read between the lines to get it.
Usually, if someone really wants to say “no” to something, they may soften it to “maybe” or “it’s alright.” In the case of being sick or having a personal issue, most people will smile and brush it off when asked about it as to not ‘burden’ those around them with ‘negative’ emotions.
The Japanese are also prone to flattery. Most common case for gaijin would be people will tell you that your Japanese language skills are great when your Japanese is completely broken.
Many foreigners may possibly take such things to heart and face value, only to later be subjected to feelings of insult.This is the source of much cultural misunderstandings. In Japan, it can be considered rude to be direct with people. In many Western cultures, it can be rude not to be straight to the point.
So, while in Japan do not be afraid of being vague at times or uncertain. If someone passes by and greets you with a “how are you?”, a simple 「元気です」 (“genki desu”/Good), regardless of how you actually are, will typically do and you may be on your way, for an actual conversation is most likely not being started.

While there is not much finger food’ in Japan (even normal tortilla wraps at times are eaten with chopsticks…), it is perfectly acceptable to eat all varieties of sushi with your hands. Most sushi is meant to be eaten in one mouthful, so using chopsticks on some longer pieces may be tedious and thus your hands may be used.

That being said, it is, however, far more common for men to do this than women. This is most likely to keep up with the societal image of women being dainty and clean, but who knows.

When you eat hot or cold noodles, such as udon, ramen, and soba, it is considered polite to slurp as loudly as possible. Of course, in your own flat this is not a necessity, but while eating out it is the expecting thing to do. This is a method of complimenting the chief for their hard work, letting them know you enjoy the food.
It is generally quite challenging for many foreigners to become comfortable to this.