I haven't been to Hakone so can't offer information on that. For Tokyo, we stayed at two Shinjuku hotels before: Sunroute Plaza Shinjuku (
http://www.sunroutehotel.jp/htok-eng/index.asp) and Nishi Shinjuku Hotel (
http://www.nshotel.com/english/index.html). Both are reasonably priced especially when they got promo.
I dun have the link for the train time website I used but will update when I get home.
Some info on food since I love eating there:
1)
Mo Mo Paradise - All you can eat Shabu Shabu, Sukiyaki. This si a die die must go place if you are a meat lover. Its at Shinjuku (address on the link).
Call to see if you can book as the Q time is usually 30min-1 hour. Go at night and after dinner, have a walk around the wild side of Shinjuku, where u will see alot of handsome "ducks".
2)
Sushi Bun @ Tsukiji Market - You can also try Sushi Dai or Daiwa Sushi. Go early and have super fresh sushi.
3) Spend 1/2 day to 1 day at Megaweb area where u get nice Ramen at Aquacity, visit Toyota Showcase at Megaweb, take the Ferris wheel if you like and take photos of the futuristic Fuji TV Building.
Nice photo areas:
1) Roppongi Hills - Prada flagship store. Unique glass building. Nearby is Midtown Tower, a relatively new shopping area. Melt your gf's heart with super patissier@
Toshi Yorzauka (level 1) or
Sadahara Aoki (level 13). (somehow I'm back to food again...). This is the trendy part of Japan, if you like clubbing.
2) Hajuruku on Sunday morning. Visit Meiji Shrine. Catch Cosplay (at the Hajuruku bridge) and Elvis lookalike doing rock and roll (at the Yoyogi Park).
3) Shibuya - Biggest junction, trendy stores, eye candy area.
4) Akihabara - For the Otaku in u. I love going to
Super Potato. Brings back sweet memories of childhood gaming.
Lunchtime over. Add more when i go home.