This video I found yesterday, neatly sums up our entire trip. It was mainly filmed in Tokyo, Kyoto, and Nara, and we have visited almost every location in these cities that are shown here. It even has a brief shot of the Golden Gai area where we had an epic pub crawl. Of course, we didn't see cherry blossoms, or the cuteness at 1:17...
Some tips about Japan that might be helpful:
1) Whenever the dollar:yen exchange rate rises to 1:100, the country is not all that expensive. Less expensive than Europe in fact. It's possible to get airline tickets that actually cost less than flights to Europe, especially with a stop on the West Coast. There are plenty of good restaurants where dinner costs under $20 per person (that's with unlimited tea), and there are decent prepared meals and bento boxes at convenience stores for under $10. In many Sushi places, 1 piece of fish on rice or a 4-piece maki roll costs between 1.50 and 2.50. We've had a couple of luxurious "kaiseki" lunches at $40 per person, but these multi-course meals were so filling that we didn't need a sizable dinner afterwards. Most attractions cost between $5 and $15. We've never seen any mixed drink cost more than $10. Oh, and there's no tipping.
2) Flying into Tokyo and out of Osaka or vice-versa can save you a substantial amount in transportation costs (only a one way bullet-train ticket between the two cities). In such a case, you won't even need a Japan Rail Pass. Many smaller and often more convenient railways won't even accept it.
3) Renting a portable wi-fi for the duration of our trip really helped us out, b/c we often consulted the English-language train schedule site Hyperdia.com and Google Maps. It was about $100 for 2 1/2 weeks, but well worth it. Data plans may be more expensive.
4)Very important to bring comfortable shoes that are easy to slip on and off, and maybe even a pair of light slippers. You'll be taking shoes off a lot, especially in Kyoto.
5)If there's one Japanese word to learn beside "arigato", it's "sumimasen". This word can be used to get attention, apologize for being a clueless foreigner, or push out of a crowded train. In general, there's plenty of English signage in big cities, and most transportation modes are bilingual.
6) Hire a Japanese guide or make a connection with someone local before the trip to show you around, for at least a day or two.