I'm not sure how useful this will be, but with the growing popularity of anime and Japanese culture, I figured I'd contribute some information on Japanese naming and placenames.

Vasha's Guide to Feudal Japan - Language is one of my favorite resources. While it's primarily aimed at naming characters, the 'initial' and 'final characters for family names' sections are extremely useful. They include a lot of great placename elements like 'valley', 'base of a hill', 'town', 'island', 'field', etc. It also includes more specific placename elements like 'shrine', 'cellar', 'pavilion', 'district', 'iron forge', etc.

If you're looking for specifics, or you want some pretty Japanese characters to make your map look even flashier, a great site for kanji is the dictionary at Animelab.com. You can search by English meaning, romaji (Japanese word written in roman characters), kanji (logographs), or kana (Japanese alphabets). It gives you a lot of flexibility, especially by letting you find out the kanji that a word is written with, and then searching each individual kanji that makes up the word to better understand its full meaning.

Delving deeper into kanji, Wiktionary is excellent, especially for giving variation in the sound of a word. If you have a lot of northern villages, then you may find the kanji for 'snow' particularly useful (yuki). By looking up this Kanji on the English version of Wiktionary, you can find multiple readings of the same kanji. The same symbol can be pronounced 'setsu' or 'sechi' by following original Chinese pronunciation (On reading), or 'susugu' is another Japanese variant (Kun reading).

Wiktionary also gives 'nanori' readings. Nanori are readings of a kanji that are used only for the names of people and places. For example, using the 'mizu' kanji for 'water', you have the On reading of 'sui', the Kun reading of 'mizu', but the Nanori readings 'uzu', 'zumi', 'tsu', 'do', 'mi', 'misa', 'mitsu', 'mina', and 'min'.

My last two favorite resources are great for creativity. The Japanese Names section at Sengoku Daimyo has some very helpful stuff under the "surnames" section, though the kanji are images that can't be copied and pasted to the AnimeLab dictionary or Wiktionary. Lastly, the Monthly Kukai Report was designed as an aide for writing haiku but the 'Terrestrial Phenomenon', 'Celestial Phenomenon', and 'Plants' sections can be useful for placenames when used sparingly.

I'm no Japanese language expert, I really only speak it well enough to say "I don't understand Japanese", but these five websites have made it considerably easier for me to look like I know what I'm doing. I hope they'll be helpful!