I've been using Google Earth for my trip. I pinpoint locations, hotels, and stations I'm interested in so I can get an idea of distance, convenience, etc. During the course of my research I found my choice in hotels changed often, many times to a hotel I had marked down previously, but never took too seriously at the time.
I also picked up this book:
According to reviews on Amazon
(click here) this book is highly recommended for Tokyo. It's a street directory with an index for everything that is marked on the maps. I was initially going to print out a stack of maps for the places I was going in Tokyo, but now I don't need to.
If you plan on staying at a 5-star hotel, whether just one night or more, try
WhataHotel.com. For many 5-star hotels they are able to offer various perks like discounted prices, free room upgrades, etc.
When booking more reasonably priced hotels, try places like asiarooms.com, but don't forget to check the hotel's own website as it may be just as cheap or in some cases cheaper.
Read up about the train and subway system. Also look into getting a Suica card, which is a smart card for rail travel. We use an equivalent here in Australia, and its so much easier than buying a fare everytime. There's the popular Suica + N'EX package
(click here) which gets you a Suica with 1500y on it, plus a trip into Tokyo from Narita Airport.
Prizm