Travellers often avoid Japan because of it's reputation for being expensive. This was certainly true a decade or so ago, but these days it's quite the bargain.
We visit Japan fairly regularly and go to get our fix of two things: the food and the onsen (hot springs).
I have been greatly privileged because I have always been taken to these Spa's so have never had to find these experiences myself, but they are always quite an experience but the best of them leave an indelible impression.
Some of the ones that spring (sorry for the pun) to mind over the years are the time we were trekking up in the mountains, Akadake (Red Mountain), and came across one simple onsen which was a simple bath cut into the side of the mountain with water bubbling up from the volcanic rocks below: the damn thing was quite memorably hot, so hot in fact that even the Japanese couldn't get into it, or at least stay in it for more than about 10 seconds, which is saying quite something since the Japanese like their baths HOT!
Another time we were in a Spa on Hakone with Yuki's family and our children and the Spa was created from an enormous rock they discovered when building the foundations of the Spa. By huge I mean we are talking about a single chunk of rock about 5m x 4m x 3m. It was so big you needed a ladder to climb up into it. The bath was constantly fed from two pipes made from bamboo with cold water running down one and hot running down the other and the excess just overflowing onto the rocks below. But that wasn't what was memorable about this occasion: I was there with my three year old son and was in the bath along with another Japanese family and some other local men when a small brown turd floated to the surface. Obviously Riu found it most pleasantly comfortable! You have never seen me move so fast! The Japanese take great care in bath house etiquette and this certainly didn't fall within that behaviour! Incredibly, nobodu noticed, or seemed to. Maybe they were just being polite to a gaijin.
Nakedness in this context, stripping off with loads of men and boys (including my father-in-law) and being the only guy with white skin in any of these places, has never been much of a problem with me. Even the mixed Spa's, yes, men and women together, which can be a bit weird given the general Japanese cultural modesty.

My favourite Spa though is called 'Unryu' on the Izu Peninsular, a couple of hours by train from Tokyo. If you have two days spare it is for me the quintessential Japanese experience and one I would very highly recommend. This place gets few gaijin (apart from me), makes no concessions to gaijin in terms of food, behaviour or style, is incredibly designed and so very Japanese, has fantastic food and you come away from nights stay there feeling like you've been there a week with skin as fresh and as young as a peach.
It is without a doubt my favourite and I try to go every time we visit Japan.

For more information on Izu and it's attractions, including where to stay, try the Japanese National Tourist Organisation