Travel Sites
Japan
Inside Kyoto (great site for visitors)
Kyoto Guide (tourist guide, helpful monthly events)
Deep Kyoto (lots of information about Kyoto by locals)
Kyoto Journal (online journal of many interesting topics, not always about Kyoto)
Yakumonkey (the site for everything you want to know about visiting Yakushima)
Yudanaka Snow Monkey Park (lots of information on how to get there, what to do there, etc)
Jcastle (a guide to Japanese castles)
Japan Visitor (all things Japan, but I like it for festival information)
Hyperdia (check your rail times/prices here)
Tocoo (cheap car rental)
Tofugu (everything you want to know about Japan, bring a sense of humour)
Falling Off the Map 