Other popular websites in Japan include Mixi, Hatena, and Livedoor. They are all social/blogging websites.
Japan also has its share of portals: Infoseek, Excite, Yahoo, and Goo (the first two having succeeded in Japan where they failed in the US).
2channel seems to be enormously popular, though. I met a 26-year-old Japanese student in transit today and asked him about it, and he was surprised that the news of it had got to the U.S.