I always felt like Japanese were fairly tolerant to foreigners compared to most countries.

Indeed, a day doesn't pass where I don't hear a terrorist joke.

I think that is an understatement of epic proportions.

You can find discrimination in a glass of water if you want to.

To say blame racism because there was an empty seat on the train is stretch. There are plenty of times I have chosen not to sit on the train, and never has it been because of the race of the person I'd be sitting next to. As self-important as you might feel as a foreigner in Japan, get over it quick.

The only people that get bad service in Japanese restaurants are bad customers (i.e. ones that don't speak Japanese and assume Japanese all speak English).

Considering there are some countries where white people are kidnapped and murdered just for being white, complaints about the treatment you get in Japan are growing a bit lame.

Agreed 100%. I've noticed the baby-like complaining here too.

I think it's very hard for a typical white boy who's been a dominant race in his country, to all of a sudden become a minority in another country. If you accept the FACT that this WILL happen before you go (and not let it get to you) then you'll be fine.