Manners are culturally biased. Even more than that, they depend on individual sensibility.

Here are a few things the average Japanese tend to do and which I personally find ill-mannered. As you read this, remember that I am not American and even as a European, probably not from the same country as you, and even if you were, you surely don't have the same social background and personal sensitivity. As a result, you may find that other Westerners behave the same way or even worse than Japanese, but these are things I don't like and don't do.

1) Being loud in places like restaurants, cafes, etc. Especially laughing very loud. This is true for most people, from little children shouting and running, to groups of teenage girls, to business people to women on their 50's or 60's. I don't mind laughing in a movie theatre, but not in an expensive restaurant. Japanese tend to be amazingly quiet in cinemas and too noisy elsewhere.

Interestingly Japanese seem not to be very sensitive to noise, and the one I know do not care much about being quiet when people are sleeping (eg. coming back late and talking loud on the phone so that even the neighbour can hear).

2) People carrying an umbrella when it is (almost) not raining. What can be more annoying on a crowded pavement/sidewalk, especially when you are riding a bicycle and those umbrella-carriers do not care about people around and suddenly wave it into your face or arm.

In general, I found Japanese to have a bad "street behaviour", not caring at all about other people, like when 5 people walk side by side taking all the pavement for them and you can't pass when you come opposite them, but they won't open up.

3) Pushing people to get in or out of the train. Shall I also mention men groping women ?

4) Slurping noisily their tea and their food (not just ramen, but everything). This is particularily true of elderly people.

5) Touts and sales people. These can be quite tenacious. At the very moment I was writing this thread, one of them came and rang at my door. I don't open anymore as I get them at least once a week, to sell goods or try to convince me to repair my roof. Really annnoying, especially when you open, they see you're a gaijin, they feel embarassed and don't not what to say, but explain anyway, then I tell them I don't need it, but people from the same company come back 3x the same month ! Won't they understand ?!