Favorite underrated experiences & hidden gems

We're visiting Japan for a week in November, and I'm looking for something memorable that I haven't done before. What are some memorable 24 hour (or less) experiences that don't normally appear on the regular itineraries for first-timers?

I lived in Japan for 18 months a decade ago, and have been back for a couple visits. There are tons of charming and outstanding attractions and experiences in Japan. I'm looking for something unique and new that will be a highlight of my short 7-day visit.

Some examples from my personal favourites (which tend to be Kansai-biased):
Kinosaki-onsen
Fushimi Inari
Kobe Luminarie display in December
Hanshin Tigers game
Temple flea markets
Koyasan
Hakkone
Yakiniku

Maybe these aren't "must see" attractions for every itinerary, but I thought they were really memorable unique cultural experiences for me!

What's on your list of underrated personal favourites and hidden gems?
Naoshima? Nikko?

Nikko is hardly "hidden", it's currently front and center on JR East's English website, for example, and it's the 15th best ranked spot on this website (and the 11th most visited).

Enoshima! I really liked it, actually moreso than Kamakura. And Karuizawa (it isn't just shopping). And Hikone. And Kamikouchi. But a lot of it is just where we had a great time, usually because of the people, rather than the place itself.

I haven't been there yet but Tobu World Square looks really cool.

http://www.tobuws.co.jp/default_en.html

It's got scale reproductions of famous buildings from around the world.

If you like amusement parks, skip Tokyo Disneyland and Universal Studios Osaka and head directly to Fuji Q, which is great. Seeing Mt.Fuji from top of a rollercoaster is amazing.

From my 1st trip I tend to find Fushimi Inari as one of my best experiences, but since we are talking about underrated, let me say that the Miraikan (National Museum of Emerging Science) in Odaiba is absolutely amazing. Also in Tokyo, and recently featured on this site, Design Festa is great for design and cutting edge independent art, and their event twice a year is Awesome and an absolute must if you are in Tokyo during the weekend it's held.

Also, technology, anime lovers must go to Den Den Town in Osaka. Sure it isn't as flashy as Akihabara but tended to like the place better.

if you are a fan of rabbits or simply want to be surrounded by them, theres Okunoshima

A stay at Hattoji Villa is one for me
http://www.international-villa.or.jp/villa/hatto0904.htm

The Mimasaka area in northern Okayama is also great. Great onsen, food, nature, and nice cultural sites as well without the crowds.

The art islands in the Seto Inland Sea, particularly Inujima, Teshima, and Naoshima.

All of Shikoku tends to be underrated and underexplored, but it has impressive castles and lots of interesting historic and natural sites.

Takahashi is excellent. If you have time to also visit the Fukiya area, Id recommend it
http://www.japan-guide.com/e/e5775.html

In Kanto, Sawara is a nice historic area of Chiba
http://www.japan-guide.com/e/e6406.html

Sakai in Fukui Prefecture is excellent. It has the famous Tojimbo Cliffs and Maruoka Castle.

Actually all of Fukui Prefecture is underrated. It has a lot of great sites, like Eiheiji Temple, Ichijodani, etc.

Hmm, there are so many places. Yanai in Yamaguchi, Ikkyuji Temple in Kyotanabe Kyoto, Kizugawa&s stone Buddha trail, most of Wakayama Prefecture, Izushi, etc

The plant conservatory Sakuya Konohana-kan in Osaka is quite underrated, in my opinion. It's not likely to be a major highlight of your trip, but if you happen to be in Osaka it's a very enjoyable way to spend an hour or two if you like flowers and plants. Easy to get to on the subway. I really think this place should be more famous (like the aquarium), but I'm just as happy that it doesn't see hordes of tourists. Last time I was there, they were having an azalea bonsai exhibition in their central hall and I really got my money's worth (it isn't terribly expensive anyway). It was excellent.

If you like Japanese gardens and happen to be in Nara, another underrated spot is the Manyo Botanical Garden (aka Gardens of Kasuga Taisha). Most people go right by it and don't even know it exists. Very nicely maintained and historically interesting.

My approach to Kyoto is to skip all the famous places and pick one or two (or at most three) of the smaller temples each time I visit that city. There are a great number that are worth a leisurely stroll-through, and while some of them are not as large and lavishly maintained as the famous places, they offer a level of serenity that's just not reachable any place where there are mobs of tourists.

Adding to a couple of previous posts, I think Osaka itself is very underrated, as most people only seem to cater for Tokyo and Kyoto, and then start to add things aside (Nara, Hiroshima, Kanagawa...) from there. To me is a really wonderful city, full of life and I like people much more than in Tokyo.

When you say 24 hours, I assume you want to leave and return to your hotel in some major city within 24 hours? Well rules out a lot of the lesser visited but amazing sites in the countryside, (e.g. Akiyoshido, Takachiho, Kumano, Dewa Sanzan)

Ise Jingu and Yamadera are doable as day trips from Kansai or Tokyo respectively, assuming you take the fastest trains. Hiking up the three shrines of Togakushi in Nagano are also doable from Tokyo as a day trip, but beware the infrequent buses.

There are lots of interesting suggestions that I have never heard of before!

For the sake of this request, I consider "up to 24 hours" to potentially include an overnight stay, based on a trip from Tokyo or Kyoto/Osaka/Kobe.

With fast and efficient transportation networks, Japan seems to have a large number of these convenient getaway destinations. Some are better-known among foreigners than others.

I thought this would be kind of tourist-trappy when I planned it, but Monkey Park on the outskirts of Kyoto was actually a lot of fun. You get a great hike to one of the best views of Kyoto and feed monkeys. The monkeys are hilarious to watch. The staff was quite friendly as well.

One of the best parts is that is brings you into the very pretty Arashiyama area where many of the other sights are free. I highly recommend seeing the bamboo groves close to dusk. Very beautiful area, very memorable.

http://www.japan-guide.com/e/e3912.html