Japan, Korea and China all share a violent past, and events such as Koizumi visiting the Yasukuni shrine (
http://en.wikipedia.org/wiki/Yasukuni) often aggrivate those tensions. Japan has done some horrible stuff to Korea and China, but most young people here (I'm an American in Japan) don't care.. it's just the older, Nationalistic politicians who have too much pride to change things. For example, the Chinese protests over the Japanese textbook that omitted mentioning the Rape of Nanjing (
http://en.wikipedia.org/wiki/Rape_of_nanjing).
However, America also has a pretty fucked-up past with Japan, and I'm glad that most Japanese don't try and blame me for the atomic bombings of Hiroshima and Nagasaki - something I had no part in. But I've seen in high school surveys where Japan was much more favorable to Americans over their Asian neighbors, so it could be a biased observation.
Of course on 2ch there's going to be racism - just look at /b/. Yet, I don't think that many of these people are serious at all, but just looking for a fun time to mercilessly bash one another for no reason at all. No doubt the effects of Anonymity and groupthink are the same for the Japanese and Americans alike (not trying to exclude the other English-speakers here). It might be the same where you can enjoy a racist joke in private among friends, even though none of you harbor true hatred against the people you're making fun of.
Then again, I'm not Japanese, haven't lived here that long, and I've only talked to younger Japanese people, but that's my impression.