[Nyororin]

I absolutely hate being mistaken for a tourist, but am going to side with MMM on this one.

For one, in the case of being mistaken for a tourist - the comparisons that are being used are completely skewed. Assuming you are a tourist is not a negative assumption. It`s a pretty neutral one. Being a tourist doesn`t mean you`re assumed to be "inferior" - it just means you`re a tourist. The other examples you are tossing out are linked to negative issues.

Remove any racial issues, and imagine that you work in a cleaning shop. For the past so many years you have worked there, every person who brought in a red coat to be cleaned asked to take advantage of the free offer for bleed protection. Chances are, after a while, you`re going to start just adding the service on whenever you see a red coat.
Is this discrimination? Are you judging the coat, assuming it is going to bleed color? Or are you just adding on the free service that everyone else has asked for so far?
Assuming that people want the service is a far better option than assuming they may not want it, then being complained about later because they didn`t know it existed.
Chances are, with the discount you were given, people who later found out that there had been a discount but didn`t receive it complained. Who is going to refuse an offer of a discount? What is the point of asking? In a clothing store (not "designer"), those type of discounts aren`t the norm. There is a fair chance that if someone is a tourist, they may have their passport on hand when shopping for very expensive things - but maybe not normally priced clothing. Potentially lose business by telling someone there is a discount but we need to confirm your visa, prompting the person to possibly stop buying to return later with their information (I know everyone is supposed to carry their passports around, but the reality is that most are stored away in hotel safes). A customer that leaves is likely a lost sale, as a tourist may not have the time to come back.

And this is once again where you're saying it's okay to judge us just because there's less of us.

99% of the westerners I meet in Japan are tourists or here for short term stays. Is it wrong of me to assume that they are not here long term until I see some indication otherwise?
For someone who has lived in Japan for years and years, who has all their life here, who owns a home here, etc... Someone here for a year on a study or teaching stint is hardly different than a tourist.

I don`t know how long you`ve been in Japan and how long you are staying - but it`s kind of funny how the people who throw the biggest fits about issues and toss out the "I pay taxes too!" thing are the people who go home after a year or two.
I`m going to make the horrible and awful guess that you probably looked like a tourist - but not because of your race. Long term residents simply do not look like tourists, and tourists do not look like long term residents. In the same way that it`s pretty famous for a New Yorker to be able to spot a tourist or new resident to the city, it`s not all that hard to spot the differences between someone who really lives in Japan and someone who is here on the short term.
I think this is the difference where I am spoken to in Japanese, quite normally, while a friend who has been here for close to a year but plans to leave soon constantly gets the tourist treatment. We`re both the same race, not all that different in coloring (although I think her eyes are blue while mine are a lighter hazel color), and both have mixed race children... But the treatment is significantly different. There is indeed a tourist "look".

Poor service to me would be speaking to me in broken English as I'm fully well speaking in Japanese to them.

An honest question - how good is your Japanese? How clear is your accent? This makes a huge difference in whether the other person decides that attempting communication in English would be more efficient than continuing in Japanese. I can`t judge in your case, but a lot of people don`t realize that their Japanese isn`t as clear as they think it is... Just like the other side doesn`t realize their English isn`t as clear as they believe it is.

Or being heckled by people on the streets who specifically target gaijins for their shops/wares.

Targeting the group most likely to buy sounds more like a good business decision than "racism" to me. People are heckled on the street regardless of race - the shops/wares that are targeting you because you`re a foreigner are doing so because foreigners are most likely to buy whatever they are offering. Should they target a market they don`t sell well in?
Is it wrong for discount airline tickets to be advertised in English language magazines? The same idea is in play. OMG! It`s racism! They`re assuming I want to travel outside of Japan because I`m a foreigner - shame on them!

It is understood that rice is a major staple in the Japanese diet, but with that type of connotation, the question is an ignorant one.

MMM gave an absolutely wonderful example. That`s a normal question, asked all the time, and one of the questions people study to answer in English class.
You`re the one reading racism into it.

Really, you may not realize it, but you are indeed dropping into disgruntled territory. I don`t think anyone realizes it at first, if ever. But you are pulling out the exact complaints that are repeated over and over and over by the short-term-but-longer-than-tourist crowd who first realize that Japan is NOT a melting pot and that they are ALWAYS going to stand out to some extent.