Accommodation is one of the big keys for your traveling.
Some people give great importance to perfect place to stay, some others try to save their budget from beds or coaches only for sleeping at night.
Some guesthouses welcome you with warm friendship, some hotels proudly serve high quality meals and hot springs, or some heavenly ryokans are ready both of those for you. If you find such, it just make your day.
In any case, you most probably want to select your accommodation carefully. I believe some of below listed sites are helpful.
Top quality hotels & ryokans
Relux
Relux carefully chooses the hotels and ryokans that they offer. Over 100 criteria for grading and experienced staff examined each venue. Hotels & ryokans are proudly offered and guaranteed lowest price. Further more, 5% of the booking cost turns into Relux points that 1 point worth 1 yen.
Support language : English, 中文简体, 中文繁體, 한국어
Wide range – Low budget to High end accommodations
Jalan
Jalan is one of the major hotel booking site for domestic trip for us Japanese. My wife and myself personally count on this site when searching low budget quality accommodation.
Support language : English, Français, 中文简体, 中文繁體, 한국어, ภาษาไทย, Bahasa Indonesia, Melayu
Agoda
The well known portal, Agoda is not Japanese company but the list of hotels and ryokans is amazing, they even listed budget backpackers hostels.
Expedia.co.jp etc other global portals also available but Agoda is apparently the most reasonable, as far as some comparison I made.
Support language : English and other 38 languages
JAPANiCAN.com
The provider of JAPANiCAN.com is a member of JTB group, one of the largest & the most popular tourism organisation in Japan. It provides you online booking service for not only hotels but also tours, and more all across Japan.
Support language : English, 中文简体, 中文繁體, 한국어, ภาษาไทย.
For particular demands
Muslim friendly hotels via JTO
Japan Traveler Online(JTO) is specifically Ryokan and Hotels online reservation website for visitors to Japan.
Support language : English, 中文简体, 中文繁體, 한국어
Stay Japan
AirBNB has huge fans, but it is not approved by Japan law at this moment. Instead of AirBNB you may try Stay Japan which is the first “legal” private accommodation rental service with in Japan. Stay reasonable in metropolitan, or find lovely experiences in a country side.
Support language : English,
OTS Hotel
Visiting Okinawa? The Okinawa local tourism agency selects the hotels in concepts of 1. Close by tourist site 2. Clean bath room 3. Good facility 4. Yummy meals.
Support language : English, 中文简体, 中文繁體, 한국어