There's so much more that you can do besides all the insipid "otaku adventure" crap in Tokyo. Do it once just for the experience, but there's a lot of deep culture and history to explore while you're there. If you've already been to the big cities, you really should consider exploring the Japanese countryside.
Around this time of year it's really cold over there, so I would recommend hitting up the onsen. I'm not sure what your travel budget is or how mobile you are in terms of transportation, but if you have a chance, go to Gero onsen in the Gifu prefecture. It's one of the most popular hot springs in Japan. Or go to a
routenburou (outdoor hot spring). The feeling of bathing in a hot spring outdoors while it's snowing is unbeatable.
If you're at all into the history of Japan, while in Gifu you can also visit the site of the Battle of Sekigahara. It's where arguably the most important battle in the entire history of Japan was fought. That was the battle that united Japan as a single nation. It's not much to look at anymore, just a bunch of rice fields and an elementary school nearby, but it's a pretty poignant trip standing on soil where the blood of tens of thousands of samurai was spilled. There's a legend that Miyamoto Musashi also fought on that battlefield.
Just next to the town of Sekigahara is a smaller town called Kamiishizu, where I lived for 3 years. There's a renowned pottery master named Tabei Sensei there. You can also see performances by the local taiko group,
Mondeko Taiko Dan. There's also several teachers who give tea ceremony demonstrations, calligraphy demonstrations, flower arrangement demonstrations--and not just in Kamiishizu but in just about any small town outside of Tokyo.
If you want to go to off the beaten path, try a trip to Koya-san. You can't get there by train, you have to take a bus to the foot of the mountain and then take a cable car all the way up. Monks live at the top of the forest mountain and you can see graveyards that have been there for over 500 years. Oda Nobunaga is buried there. The sesame tofu prepared by the monks is really good too.
Don't know if your girlfriend would approve, but you can try to get
nyotai mori, which is eating sushi off a naked woman. It's actually illegal in Japan, so you'd have to know someone who really knows his way around the seedy parts of town. The drawback is that it's really expensive, the portions are small, and there are two bodyguards in the room with you at all times making sure that you don't touch the girl more than is necessary for you to eat the sushi. Oh, and they don't allow you to take pictures of you enjoying it
Still, it was a unique experience for me.
Too bad you weren't there over the summer, because that would have been the time to climb Fuji-san. That's physically one of the hardest things I've ever had to do. We started climbing at 10pm, climbed all night and made it to the top just in time to watch the sun rise. Right now the peak is covered in snow and climbing season won't open up for another several months. If you ever get the chance though, take a camera with a panoramic lens with you if you have one.
One more suggestion I have off the top of my head is to take a trip up to Sapporo in Hokkaido in February for the
Sapporo Yuki Matsuri (Snow Festival). The Japanese SDF builds gigantic, detailed ice sculptures of anime/manga/video game characters, TV personalities, even life-sized castles. When I was there, there was a full-scale sculpture of Nagoya Castle, which was really impressive. There are a lot of Nintendo-themed sculptures too, so maybe you can take a pic and show it to us on GBAtemp.
Oh, and anyone who is thinking of buying rare anime/merchandise in Japan, you'd be better off importing it because believe it or not, it's actually more expensive to buy that kind of stuff
in Japan. The reason why is because otaku culture is so prevalent there that there's a huge market for it and stores can markup the prices because people
will buy them no matter how expensive it is. But just to indulge the otaku lovers, you can try to pick up one of these while you're there:
http://www.geekologie.com/2008/10/coming_s...rverts_webc.php