I go to Japan every couple of years, I love it there. My most recent trip was last year, and I climbed Fuji overnight to watch the sun rise, it was amazing!
To give you an idea, we normally do a couple of weeks, with 4 - 6 of us, and manage to visit 4 or 5 major cities or so. It's a LOT of travel though.
If street photography is your thing, Tokyo is the best, but Osaka and Kyoto are good too. If you want historical stuff like shrines, Kyoto is where it's at, and Nara is good too. I can recommend a few really good places that I've been:
Miyajima Island, it's in the top 100 places to visit before you die, and with good reason. It's a beautiful island off the coast near Hiroshima. IF you go, stay overnight in one of the island's many traditional Ryokan. There's a mountain there you can climb too, with great views across to the mainland, as well as the famous floating shrine and Torii gate.
The peace gardens and museum at Hiroshima are beautiful, and very moving. I imagine, the Dome (the only surviving building), which is pretty eerie at the best of times would be even more striking in the winter.
If you go to Kyoto, check out the Golden Shrine, the Silver shrine, Ryoan-Ji, Kyoto Castle and Gion. There's also a fantastic giant Flea market once or twice a month at one of the temples not too far from the main station.
Osaka has the castle, and an excellent aquarium.
If you want a good day trip and you're in Kyoto or Osaka, consider a day trip to Himeji Castle. It's the best surviving original castle in Japan, and if you've seen a film set in Japan with a castle in it, the chance are it was Himeji Castle.
Kamakura is a good day out from Tokyo, it has a wonderful small town feel to it, and there are some beautiful shrines there.
I don't know if giant robots are your thing, but in Odaiba in Tokyo, they have a life sized Gundam robot, which is light up at night, and is very cool indeed.
As others have said, the street food in Japan is amazing, and the Sushi is awesome. I'd also recommend trying the regional specialities of any region that you visit!
As others have mentioned, the further away you get from Tokyo, the harder it is to get around if you don't speak or read Japanese. Do your research in advance, it'll make your life much easier! A lot of the other major cities are easier to navigate now than they were on my first visit in 2005. Most of the major bus stations will have bus schedules in English if you ask.
If you plan on getting around by train, consider a JR Pass, you have to buy them before you go, but they allow you unlimited travel on the JR trains, and some of the ferries as well. If you're doing more than one or two long journeys, you'll save a ton of money. You can't use the fastest bullet trains though. Driving is OK, but again, it can be a bit intimidating if you can't read any of the road signs!