Useful links
Excellent website for finding restaurants; their reviews are generally on the money. Covers Tokyo, Kyoto and Osaka.
Events, eating and sights in Kyoto.

Asking for Trouble
This is an excellent guide to Tokyo shopping, with a strong focus on the crafty and kawaii. Excellent descriptions and directions to hard-to-find shops. It's all online or you can buy the printed zine to take with you.

Tokyo Art Beat
Comprehensive site of all things arty and design-y in Tokyo, with listings by popularity and date.

Hyperedia travel
Useful site for finding your way around the sprawling Japanese public transport system.

Japan rail pass
If you're planning on doing much travelling around Japan, you will probably save money by buying a Japan Rail Pass, which allows unlimited travel on most trains for 7 or 14 days. We bought ours from Inside Japan Tours, and you can also add a Pasmo card for Tokyo metro travel.

Superfuture - Supertravel
Find the coolest shops by area with Superfuture's interactive maps.

Quirky site with more unusual bar and shop listings.

CNN Go: Tokyo
New but informative site with current events and the newest shops and restaurants.