Nikki
4SQ SU Japan: Don't miss here if you come to Harajuku. We recommend weekdays.
Kira: You have to onsen! This is basically like an amazing theme park where you can enjoy all the hot baths and feel like a local.
Kira: Old-school Japanese coffee shop - really a magical experience, stick around and stay a while and try the chiffon cake.
Josh: TINY bars, lots in this general area. Usually they seat like 6-10 people. Lots of fun little alleyways to go down.
christian koch: photo gallery and publisher with lots of daido moriyama books (and others)
Kyosuke: Best location directly connected from Marunouchi South Exit of Tokyo Station.
4SQ SU Japan: In case you visit Odaiba, don't miss here. The life-sized Gundam.
4SQ SU Japan: A tiny garden at the rooftop of the mall but great scenic view of the classic Tokyo Station.
4SQ SU Japan: Fresh Japanese style breads you've never had. Located near Apple Ginza. For snacks.
4SQ SU Japan: Nice coffee place for chilling in Omotesando. Near Kiddy Land.
4SQ SU Japan: One of the most complexed and scrambled crossings in the world. It's an entertainment. You'll know what I mean after you visit there.