Quite a few ryokans do not show up in hotel searches. Some ryokans only accept bookings through their own website or by calling them. Others withhold top room categories from major booking engines. Finally, a handful of ryokans do not even publish details of their rooms (Tawaraya is the perfect example.)

Usually, however, if you go to the ryokan website, there should be a link to a reservation system. If you are viewing the English version of the site, many of them will take you to a designated booking engine (often booking.com.) I've found that some of the English-denoted room names/types don't correlate well with the Japanese room names, making it quite confusing.

In Japan, the most reliable (and expansive) booking site is ikyu.com. Sadly, it's in Japanese only. Japanican has a large number of ryokans that are bookable from their site, although they don't always make the Tokubetsu Shitsu (special rooms) available. It's all very confusing, yes! Which is why many foreign travelers rely on the Ryokan Collection to assist with bookings. Their ryokan choices are severely limited, although some of the top properties are part of the Ryokan Collection portfolio.

P.S. - I'll be adding comments on more properties over the coming days and weeks, so stay tuned.

It's all confusing, I know! Stay diligent, and you will be rewarded. Trust me, it's worth the effort!

As RichardInSF mentioned above, it's hard to compare. Most rates include half-board meals, and are per person rather than per room. In general, for nicer rooms at top ryokans they usually start at about 30,000 Japanese Yen per person (I'm not going to quote in dollars, given the crazy exchange rates at the moment) and can blow past 100,000 Yen per person for the very top Suites/Villas at places like Asaba, Chikusenso, Takefue and the Fufu properties. In fact, many ryokans in the Hokuriku region boost their rates during Red Snow Crab season - Bouyourou commands a 200,000 Yen per person rate between November and March (I'll find out if it's "worth it" when we visit this November; it's almost triple the price of Nishimuraya Honkan, which has been an annual pilgrimage for us.) Note, however, that a kaiseki meal at Aman Kyoto's Taka-An restaurant goes for well over 30,000 Yen per person, and Japanese breakfasts can easily exceed 5,000 Yen (and up) at luxury hotels. You CAN, however, book a non-suite and still have a wonderful time. Some entry level rooms have just one room that serves as the living room, dining room and sleeping room (they'll lay out futons at night.) It's not quite a luxury experience but it will still be an incredible cultural experience.