I will continue to update this page as and when I find other useful websites. Do feel free to recommend other sites you have come across during your holiday planning to the Land of the Rising Sun.
Note: Always compare hotel prices across different websites. Sometimes you may even get better deals if you go to the hotels' websites (provided they have an English version).
Good deals on hotels and detailed information.
Good deals on some Japanese hotels
Quotes in USD, but some good deals
Excellent site not just for hotels, but ryokans and tour packages
Specifically for booking traditional ryokans, most of which come with onsens.
Always, always, check out the reviews of the hotels you have identified, or get to know recommended hotels for your destination.
Do note that other private train operators will also have their own websites.
Cannot go without this!
JR East - For Kanto/Tokyo region, including links on Narita Express
Nartia/Haneda limousine bus
Kansai Thru Pass for Osaka, Kyoto, Kobe, etc.
Osaka Municipal Subway
Travel within Kyoto is mainly via bus, and not trains!
For day trips and other tour packages
Tokyo restaurant guide
Singapore blog, but blogger went to Japan and made very interesting recommendations, so if you are big on food like a typical Singaporean, go read it.
Excellent source of places to visit
Just discovered this. Fabulous site with almost everything.
Another great site chockful of information.