My favorite ryokan out of those I have been to so far are (ranked in subjective order of well-roundedness between stay/food quality):
- Asaba in Izu Shuzenji - great balance of small but high-end ryokan, delicous food, great onsen, and homey service (and easy weekend trip from tokyo).
- Kamenoi in Yufuin - excellent stay and especially the rooms and onsen are very nice, their homemade noodles were memorable
- Kanamean Nishitomiya in Kyoto - amazing wine selection, great food and very approachable chef/owner that made for a memorable night - room nicely decorated with garden view, but food is served in a separate (private) room and not an onsen place
- Beniya Mukayu in Kaga onsen - very different vibe of what a modern artsy ryokan can feel like, food is nice as well but served in a restaurant
- Hoshinoya Karuizawa, a bit more "packaged" but the food was nice, especially I don't think I had better hotpot in Japan then there - nice experience

Will defenitely try Nishimuraya Honkan if I have the chance, seems quite nice!!

Thanks for this nice list! I also liked Takinoya in Noboribetsu. Great place for winter, food is local and so delicious.

We enjoy our time at Yoshikawa Ryokan in Kyoto - we've already booked our 3rd stay with them for our upcoming trip

Thanks for the recommendations everyone!

@kk1337 I've heard great things about Kanamean Nishitomiya too, but never visited because of all the choices available in Kyoto for dinner. I hope you like Nishimuraya Honkan though! I saw a poster on the main Q&A thread say that he was disappointed, and saw alternative recommendations for Bouyourou (both here and another forum, Flyertalk) for crab season. But the latter's way out of my price range :p

@JJ What about Hirasansou or Miyamasou?

@DanielfromHK Does Hirasansou still take overnight stays? Or is it now operating as a restaurant only?

I’ve actually considered Miyamasou, but couldn’t find them on Ikyu or any online reservation site. I’m glad they finally renewed their website though, and it now has an email address. Previously, one would have to call…

@JJ Miyamasou actually has an email address when I tried to book back in 2014. They even used English for communications!

For Hirasansou, I am not sure if it is just a restaurant now. On their website, it doesn't look like there is reservation for staying anymore. Maybe they have changed

Yeah I noticed that page on stays on Hirasansou’s website went missing too. A bummer because I haven’t yet seen reservations open up on Omakase either.

Funnily enough, I just hit Google Translate on Miyamasou’s website, and it said that reservations by email are no longer accepted. Right after which they provide a reservation email address, most puzzling :p. (Although in this day and age, when even once-“reclusive” ryokans like Iwanoyu have started taking last-minute reservations online, you wonder why they don’t at least put an availability calendar online).

Wanted to update this thread with some notable food-focused ryokan experiences I’ve had recently:

1. Kanaukan, Matsumoto
A hidden gem, probably the best kaiseki meal you’re going to get without driving to Mumyo, 50km away. The chef’s fried ebi imo with yuzu miso was the best rendition of ebi imo I’ve ever had, and the gingko soup was also revelatory. All the other dishes were decent, but nothing mind blowing. Happy that they included the local specialty of basashi on the menu, for busy folks with no time to try it in town.

2. Byaku Narai, Narai
The dinner menu was supposedly a collab with Zaiyu Hasegawa. I’m normally sceptical of celebrity chef collabs, but the food here was pretty good. You get plenty of river fishes: koi was prepared as a fried fishball with a nozawana sauce (far better than serving it as koi no arai), and the yuki masu sashimi beat out 3 others we had in the same week. You also get gibier, like a boar meat manju, and there’s a special bear menu if you order in advance. For a sake brewery, it was odd that the alcohol pairing was 2/3 wine, but I guess one can go a la carte in the future.

3. Hatago Wakatsu, Omihachiman
I really wanted to like this place more, but the food wasn’t as good as Kanaukan and Byaku. The chefs seem to be rather inconsistent with seasoning — e.g. the A5 wagyu sirloin shabu shabu would have been so much more flavourful with just a bit more salt. The beef rump preceding it was over-salted instead. There was also too much of a focus on smoked flavours, and my palate got tired after awhile. The ingredients used here were actually more luxurious than at either of the above two places, but it was a case of the chefs not being skilled enough to bring out their full potential. While my review might seem harsh, it was still pretty good for a ryokan meal. For comparison, a restaurant like this would probably get a 3.7-3.8 rating on Tabelog if it was in Kyoto.

Asaba in Izu is said to be the ryokan that invented the one stay two meals (1泊2食) model.

Visited in 2018, the best 2 day-stay I've ever had. Food was fantastic, service was another level. Ryokan was super well maintained and had a home-like vibe. The town and its history is fascinating.

Highly recommended.