Some discussion from our mailing list in summer 2011.
“I think we should do a THS recommends binder and pdf. to have to give out at the space.”
– Lauren
Richard's Suggestions
DragonQuest Cafe in Shibuya
Akihabara, of course, for electronics / Gundam Cafe / Linux Cafe / Super Potato
Harajuku for costumers
Nakano Broadway
Asakusa (sensouji)
Kamakura for the daibutsu
Torsten's
Kamogawa to demonstrate that Japan isn't just over populated concrete hell?!
For people who like to travel north….
Matsushima is very nice.
Zao mountain is nice too.
Guess in general any other city which happen to have a festival during the visit. Japanese processions are by any means worth a visit.
Lauren's
small more eclectic neighborhoods
Kichijoji
Nakameguro
Jiyugaoka.
Tour of a few great food spots.
Tsukiji of course.
Book district in Jimbocho.
Zachary's
As far as nerd friendly tourist attractions go, I found the Ghibli museum to be quite memorable (even as someone who had never heard of Ghibli before visiting Japan).
Also on Odaiba the Sony Explorascience (though more for younger crowds)
National Museum of Emerging Science and Innovation.