(After pointing several times ot the very nice intro about cultural relativity) I would add,

1) some people having complete and total lack of control over their small children and not even trying to get them to be quiet/sit still/not run free in restaurants or shopping centers. My favorite is not making their kids apologize for the whole "gaijin da!" comments - I don't buy it in this day and age that young parents don't know that some foreigners consider that very rude indeed. Come on, the kids are not that cute. Once in awhile it is okay, kids will be kids, but all the time? Parents, grow some b****.

2) Maybe more of a country thing, but peeing at the side of the road. Mainly old men do this, and it is more sad than rude since I have seen it about a thousand times by now.

3)Using a toothpick at the table - again, more of a old man habit.

4)Staring. I know what this is all about and why people do it, but it is a shock at first.

5)Smoking in enclosed areas. I'm all for the freedom for people to mess up their bodies and raise the cost of insurance, but smoking where others can suck your smoke is selfish and shows a basic lack of repsect for others. I don't force people to eat the junk food I carry around from time to time, others shouldn't force me to an earlier grave (smoking is still very big in Japan and out in the country).

There are more, but I will stop here.