Try to stay in a Ryokan (a traditional guesthouse) instead of a hotel.

Must-see places in Tokyo:

1. 'Tasuichi', Shibuya, standing bar
2. 'Womb', Shibuya, disco
3. Love hotels, go to the nearest one
4. 'Pepper Lunch', steak house, everywhere
5. '109 Building', Shibuya, the right place to see Japan's most beautiful women

Stay outside of the most popular areas, such as Shinjuku or Ginza and watch your hotel bill drop by more than half. You can find excellent culture off the beaten track in places like Ueno, and the hotels are around 3000 yen/night rather than 9000 in Shibuya.

Concerning advances in technology and way of life, Tokyo is your city! Akihabara is the most exciting place for the PC-expert, where Sony VAIO's and Macintosh equipment are sold side by side in benches like in a flea market!

Tokyo Park Hyatt Hotel. Did you see Lost in Translation? Yes, then you have to visit the hotel. Just take an elevator (even as backpacker!) and enjoy the view over Tokyo!

washington hotel shinjuku quite nice, in the middle of shinjuku, stay at the main complex, the annex has serious ventilation problems. at the main building ask for a room with a view on a high floor, and don't take the cheapest one, u can't turn around in it with your luggage open. you pay little more and get a lot of comfort with it. staff generally quite friendly, although there's serious need for improvement for some.

Stay in K's House in Tokyo - great location, good rates and excellent company.

六本木、新宿、渋谷 those are the places!
お台場 is also cool for sightseeing, although it reminds me of 大阪港

When they mean Room for one person only.. they actually mean it!! even if you try to pay for a Second person unless you are horse and you sleep standing in the corner then its ok!!! there is bearly space for one!!!

Get a place to sleep before you arrive unless you're fluent in Japanese !