Here is a list of some useful sites (which are in English) for living in Tokyo, or to some extent, Japan. This will be updated periodically. Feel free to give some suggestions in the comments.
Paperwork / Official
Immigration bureau – Visas, residence status and what not.
Japan Student Service Organisation – Information about studying in Japan.
Japan Meteorological Agency – Check out the weather and alerts for tsunamis, earthquakes and pollen!
Transport / Utilities
Hyperdia – Transport routing with lots of options and detailed information.
Japan Post – Postal service. Useful for checking things like postal codes.
Real-time earthquake info – Earthquake info given in English in real-time.
Shopping / Travel
Craigslist Tokyo – Japan is known for its costly item disposal. Hence, things are usually given away for free or on the cheap. Craigslist is a great place to start looking for such stuff.
Japan National Tourism Organisation – This sub-page gives a list of useful information such as discount tickets for public transport.
Japanican – Travel related information and offers by Japan Tourism Bureau.
The Flying Pig – Third party shopper for Costco goods.
iherb – Not exactly a Japanese company but great website to online shop while in Japan.
Dominos Pizza – Pizza and subs!
The Meat Guy – Meat, meat and more meat! Including stuff you can’t get from the neighbourhood supermarket.
SuperOrganic Foods – Weekly boxes of organic vegetables for those that care enough.
News / Entertainment
Japan Today – Mainstay for me every since the other JT starting charging for online reading.
RocketNews24 – Random news about Japan… and more.
NHK World – NHK news… and some useful resources for learning Japanese.
Book Depository – Another international website with better prices than local equivalents.
Gaijinpot – Some like it. Some hate it. Find out for yourself.
*Feature image courtesy of Fugu Tabetai (CC License)