I echo the sentiments that more info is needed, but I'll give you the itins for both of my trips- my perspective being that I was a Japanese studies major, (enough grasp of Japanese not to be intimidated by off-the-beaten-path places) and have a bit of an independent streak when traveling in Japan, especially trip #2.

Trip #1
2 weeks (July 2000), with a friend who knew next to nothing about Japan
Week 1- Tokyo
Over seven days, went to Akihabara, Ueno Park (museums), Ginza (Kabuki theater), Roppongi, Tokyo Tower, Shinjuku (and Kabuki-cho), Shibuya, Harajuku, Asakusa and Mt. Fuji.
Week 2- JR Rail Pass
2 days in Kyoto, then Osaka, Kobe, Hiroshima, and Miyajima.

Knowing what I know now, I would have skipped Hiroshima, and would have tried to wedge in either Nara or Himeji. Also, I would have tried to make it to the tuna auction in Tsukiji while in Tokyo. Other than that, pretty much a perfect first trip to Japan. My friend loved it! We hadn't planned our second week in advance, short of having purchased the rail passes in the US, and knowing what cities to hit. We stumbled on the convention center and the JTB travel agency inside, and booked Welcome Inns for the entire second week.

After that trip, I went to China and then returned to Tokyo to work for a few weeks. The only other thing I saw was Yokosuka and the Tanabata festival, and another festival in Azabu-Juban.

Trip #2
3 weeks (March 2004)
I was much more informed, and had made more friends in Japan thanks to the internets. I was mostly solo, but started with my sister and bro-in-law, met up with a traveling friend, and stayed with a third friend who was on a teaching program. My goals were to explore Kyushu (southern island), experience Japan as more of a local, and hit some things I missed last time. This time I booked the Welcome Inns from Narita airport before I caught the train to Tokyo.

Week 1 Playing happy tour guide to friends and family
Tokyo (mostly a repeat of last time, but now with the Tokyo-Edo museum)

Week 2 Mostly Kyushu
Nara (partied all night, walked around the temple complex at day), Kumamoto, Nagasaki, Mt. Aso, Beppu, Kagoshima, Fukuoka, Kobe

Week 3 New experiences
Miki (town near Kobe), Osaka (sumo tournament), Himeji, Tokyo (drum museum)

I knew the itinerary was ambitious, but my excitement for being back in Japan overcame my aching feet. I did nearly everything I wanted to, except I got to Mt. Aso too late to do anything there, so I was stranded for 4 or 5 hours. Didn't get to see the samurai town near Nagasaki because I couldn't get a reliable schedule ahead of time, and it was too far out of the way, managed to see everything I wanted to in Kagoshima despite torrential rains, and rains kept me from taking a day trip from Tokyo to Nikko or Kamakura. Never got into the Tsukiji auction despite one attempt from me and two from my sister (closed both times!). Just leaves more for my next trip!

I really don't know what compelled me to write all that, considering you haven't provided us with much information, but I hope you find it useful!