Tokyo Sightseeing

Seasonal / Limited

 * fireworks in summer.
 * from a boat
 * from a skyscraper
 * picnic it at Sumidagawa

Otaku / Anime theme

 * maid cafes (some are English speaking, google it)
 * Gallery of Fantastic Art in Aoyama
 * Kaiju Simulation in 清澄白河駅, near Kiba
 * Robot stores: see the Akihabara guide, or Our friend Lem's site
 * Retro video games: Super Potato, especially if you go to Osaka

Museums

 * Transport Museum in Oomiya
 * Ghibli Museum (get tickets ~1 month in advance)
 * Salt & Tobacco Museum
 * Subway Museum in Kasai
 * Parasite Museum
 * Disaster Simulation in Matsudo　in Japanese
 * interactive art at Opera City

Theme dining

 * Biohazard restaurant
 * Alice in Wonderland restaurant 魔法の国のアリス("meh")
 * dinner cruise in Tokyo Bay
 * Robot Restaurant in Shinjuku

Shopping

 * THS's Guide to Akihabara
 * Odaiba
 * Kappabashi (http://www.ganso-sample.com/shop/)
 * RC stores (in Akihabara?)

Sightseeing

 * Inokashira kooen

Aerial Views

 * Tokyo Tower
 * Cerulean Tower (Shibuya)
 * Mori Building (Roppongi Hills)
 * Tokyo Sky Tree
 * Tokyo Metropolitan Government Building (Shinjuku)

Suggestions from last summer

Richard's previous advice to Paul

Near Tokyo