BBC Weather Centre + Country Guides: Japan - Provides climate and weather information, facts and statistics about the country, along with five+day forecasts for major cities.
NOAA NWS + Japan Weather - US government site provides hour+by+hour weather conditions for the past 24 hours for major cities and locations in the country.
Weather Underground: Japan - Offers current weather conditions for a nationwide list of cities, including barometric pressure, humidity, winds, and time of last update.
WeatherHub + Japan - Links to forecasts for cities and airports from various weather sources.