I just got in last night from my 3 week stint in Japan... and was it ever great.
If you like to see the real deal, spend some time outside of the cities. Tokyo and Osaka are cool, with Osaka having far less tourists. When I travel to foreign countries, I don't usually go to hang out with other tourists, I go to see life though the eyes of the countrymen.
K's hostel was by far the best hostel chain I have been to. ever. The one is Kyoto and Mt Fuji are fantastic, I would bet their locations in Osaka and Tokyo are also great.
Overall, I thought Japan was cheaper to stay and eat in when compared to most other destinations. It can get expensive easily if you start going to hostess bars and eating at the most expensive restaurants.
All that being said, it must have been around 3 g's (incl airfare) CAD for 18 days of madness. I will be posting up pics and a bit about the bike scene shortly.
If your riding while there, stay at the riders INN, spotted around the country. Good luck trying to look up locations tho. We stayed at one, it was perfect. A shower and a room to sleep in, and a table. Nothing more.
If you want to see the country side, ride through the mountains, eat with the locals, see the real temples that aren't flooded with tourists, stay in a place with no english (i hope your japanese is good ), go surfing, swim in the warm pacific ocean waters, go to the Island of Shikoku. Incredible.
Osaka: Go to the Namba district for shopping, eating and bars. Wander around and eat at places that have only japanese people there. Go bar hopping by starting at the top floor and working your way down the 6 or 7 stories.
See spa world. You will thank me later. Trust Me.
There is a nice indoor aquarium, cool place if you have the time.
Kyoto: Wasn't all it is hyped up to be, a place for "tourists" to cross of their lists. Not sure how anyone can zen out in the rock gardens with hundreds of tourists snapping photos and chatting idly in the backgroud. Probably some where you should go, but I didn't like the fact that it catered to tourists. Sort of removes the authenticity of the culture for me.
Mt Fuji: I stayed at the K's hostel near Mt. Fuji. It was the best hostel I have ever stayed at. Not much to do at night, but during the day you can go hiking, parasailing, fishing, cycling, etc.
There are a lot of tourists here, but for some reason the places we went too, we saw none of them. Most of them were european folks staying at resort type hotels around the lake.
Lots of traditional japanese restaurants here if you spend the time to look. I love eating where the locals go to eat and drinking where the locals like to drink.
Tokyo: Take Manhattan, NYC and multiply by 6 or so. Tokyo is huge, read up and decide what you want to do. There is the electronic/nerd district, red light district, shopping district, a motorcycle district, everything you can think of district. Look it up, or use a recently published travel book as reference.
Shinjuku: Red light district, clubs, girls, shopping
Harajuku: Go on sunday afternoon to see the harajuku girls. Google it.
Shibuya: Shibuya 109. Girls Girls Girls, that shop all day and are dressed to the nines.
Rappongi: Never made it there, but supposedly the girls look for foreign men at the clubs here.
Travelling, trains are probably the fastest between places, and the above ground and subway systems are impressive. A bit tough to navigate if you can't read or speak japanese like me.
A JR rail pass can be bought, google that one too. You CANNOT buy that pass once you are in Japan, so plan accordingly.
Finally, be prepared and take a phrase book. Or if you can, do like me and go with someone who can speak a bit of conversational japanese. Very few people can speak english fluently, but if you can look and point you will manage. Learning how use the number "counters" is helpful for ordering, and being polite and smiling will get you far with everyone.
Hope that helps. Japan is a fantastic place to visit!
to go. 
