Trip planning for end of April-May 2009

My boyfriend and I are planning a 3-4week trip around Japan. We want to maximize our time in several cities with about 4-5 days in Tokyo.

What are some suggestions which places to go and what are the most economical ways to travel between those places?

With Golden Week happening during our travel, where are the most festive places to go to, and how early in advance should we reserve our accommodation?

Here are some suggestions for places to visit and how to access them:
http://www.japan-guide.com/e/e2164.html

Tokyo hotels do not usually get booked out, so, unless you have a specific popular hotel in mind, reservations do not need to be made far in advance.

Thanks Uji, that definitely helps a little. Do you have any personal favorite places in Japan that you've been to?

Do you have any personal favorite places in Japan that you've been to?

I have dozens of favorite places. Many of them are rated with two or three stars in the following sightseeing guide:
http://www.japan-guide.com/e/e623a.html

Thanx Uji~! that's very helpful with brief descriptions as well!

Since everybody is on vacation during GW, chances are that you will find good deals at business hotels in Tokyo. On the other hand, every decent resort or ryokan will be filly booked. Plan your trip such that you will be in Tokyo during GW so that you can avoid the crowd. Also, reserve your train tickets for long-haul travels around GW.

There is a flower park near the Fuji Five Lakes region with a special sakura bloom during late April to late May. It's reached by 30 min. shuttle bus from Kawaguchi-ko. The park is opened 9.00-17.00, 500 yen for entry. It is a good side-trip if you're in the Mt. Fuji area.

http://shibazakura.jp

Did you checked the tab "A-Z" at the very top of this site? It has tons of great info. including answers to stuff that all 1st timers are wondering about. This is the section I first looked at, for my first trip to Japan, years before I clicked on forum, and it helped me greatly, especially the part about train travel. You can also Google questions about each town you are interested in (look for tourist info about...)for railway schedules, maps etc. Try to first learn about all sort of places then make your own choice. Please don't make the common mistake of trying to see too many places as, months later, it will all be a big blur in your mind. It is also very tiring to change hotels every few days etc. in 3 weeks you should focus on 3-4 areas at most then, in each area, you can look at the main town then take day trips in nearby interesting places. The Kansai region (Osaka, Kyoto, Nara, Kobe, Himeji, Wakayama etc.) for example, is the Cradle of the Japanese civilization and has many many more historical sights than the Tokyo area--and lots of modern buildings too in Osaka. You could stay 3 weeks there and only see a fraction of all there is to see. If you are very familiar with Europe fast trains trains and subways-and their big crowds--you are already ahead. If not, take it easy in your planning.