First thing to point out to you is that standards at Ryokans vary wildly.

The quintessential Ryokan experience I would recommend (which will include a welcome tea, full evening meal, a soak in a natural Spring water bath, a full breakfast and impeccable and thoughtful service) is not common at all within Tokyo. It is commonly available in Kyoto, but the prices for good Ryokans are particularly steep there.

Many places, especially at reasonable prices in these two cities, that call themselves Ryokans are Hostals or basic hotels with Japanese style rooms.

Whilst I would certainly encourage you to stay in a Ryokan, I would advise you to stay in one in an area between Tokyo and Kyoto or in a surrounding area. This way, for perhaps ¥13,000 or so, you can almost be guaranteed of an unforgettable experience in a very comfortable room with outstanding food.

If you want more detailed info and a guide to etiquette you can find this here
http://www.ryokan.or.jp/index_en.html

For suggestions of where to stay:
http://www.japaneseguesthouses.com/index.htm
Is a recommended booking agency

If you are nervous or unwilling to stay too far from Tokyo or Kyoto, a couple of suggestions are:
Kurama Onsen - a short local train ride from Kyoto
http://www.japaneseguesthouses.com/db/kyoto/kurama.htm
(Which has had good reports from here)

or
Wakamatsu Honten in Narita
http://www.japaneseguesthouses.com/d...atsuhonten.htm

There is Sadachiyo in Tokyo
http://www.japaneseguesthouses.com/d.../sadachiyo.htm
But a lodging and meals plan will not be cheap - and lodging at a Ryokan without eating there would mean missing out on the main reason most of us rate a Ryokan stay so highly.
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My only Ryokan stays have been in more rural areas so I can give you no first hand recommendations for any of these suggestions. I also suspect you can find better/more atmospheric places if you are prepared to factor in a Ryokan stay as part of your trip. I'm certain you would find it worth your while.

If money is no object, then by all means stay in one of Kyoto's top Ryokans. Without knowing your budget, or what you would be prepared to pay, it is very hard to advise you.

Staying in a ryokan is an excellent way to get a traditional Japanese experience. Id recommend doing it in Kyoto for a couple of nights at most. As an earlier poster mentioned they do vary widely in comfort level but no matter what you will be sleeping on a futon on top of tatami, so it will be harder than your mattress at home! Its still a great unique experience, especially when you get your meals served to you in the room.

Wow, thanks for the suggestions!

It's definitely an experience worth having, though I would highly recommend you do so in Kyoto rather than Tokyo.

I've come across some great ryokans in Kyoto.

On the luxury end of the scare there's:

Hiiragiya Ryokan
Hiiragiya Ryokan Annex
Ryokan Shimizu
Tawaraya Ryokan
Ryokan Motonago
Ryokan Seikoro

For something more middle-of-the-range in a great area try:

Ryokan Uemura. Send faxes only to enquire about rates and availability. It's about 9,000 JPY per person per night though (plus brekkie). The fax number is +81 75 561 0377.

All the top notch ryokans have their own websites, which you can google.

Try Yoshimizu in Tokyo. The website is http://yoshimizu.com/en/ginza/index.html.

I just got back from Japan and stayed in the Ryokan Uemura and the Hiiragiya Annex in Kyoto.

Spent one night at Uemura. Really sweet place run by an elderly couple. Granny is very friendly and concerned that you're having a comfortable time. The curfew is at 10pm, so not a place if you're after a party, but it's right in the centre of old Gion. Incredible location. The street is one of the prettiest in Kyoto and is lit up with lanterns at dusk. The room cost 9,000 yen per person - it's not luxurious, but very clean and perfectly comfortable. The bathrooms are shared and Granny makes breakfast in the morning.

The Hiiragiya Annex is a different kettle of fish. Much more upmarket, with a price tag to match. Think it was about 80,000 yen for two people per night. A wonderful place though and make sure you have the traditional Japanese dinner.

I agree, the Ryokan Uemura in Kyoto is great value for money.