Reading Tsukiji: The Fish Market at the Center of the World beforehand made the actual adventure that much more enjoyable. I definately recommend reading it first although reading it after while also help to make sense of the experience. But you better hurry. It appears that Tsukiji won't be around too much longer.
I very much enjoyed Gaijin! Gaijin! and the follow up Mo Ichido. Although both books had numerous typos and the second book was repetitive, Kenneth Fenter is a good observer and describer of Japan, the Japanese people, and Japanese culture. He can tell a good, detailed story. Anyone who has lived in Japan should enjoy these books. Those going to live in Japan will have much to learn from them before going. In Suteindo Grasu, Stained Glass: An American Family in Japan, Fenter finishes the story of his adventures in Japan. The book is different than the first two but will still be enjoyed if you read and liked the first two. It will also be of interest, on a stand-alone basis, to those who haven't read the first two if they are planning on doing business in Japan or if they have an interest in Stained Glass.
I also enjoyed Untangling My Chopsticks: A Culinary Sojourn in Kyoto. My favorite parts were the author's descriptions of Kyoto rather than the food and cooking. The book is about half travelogue and half kaiseki/cookbook. As one who prefers donburi, yakisoba, etc. over seafood any day, I wished it was 100% about the former instead. Perhaps you will wish for the opposite. In any case, if you are into food or into Kyoto, or both, check it out.
Although Yankee Hobo in the Orient is now very dated, it is (or should be) a timeless classic. Written by a libertarian who visited Japan, Korea, and China before World War II, the adventures are amusing and insightful. The style is somewhat similar to Mark Twain. Even though I shared the author's political views he beat his political horse to death after just a few chapters and could have done without the continuous preaching throughout. If you can get past the banter, the stories are incredible. This is a very fun read.
Kyoto: A Cultural History is a highly recommended read for anyone going to Kyoto or who has been there and wants to understand it better. The book isn't about the place so much as it is about its history and the people who have shaped it. It isn't really a guide book although it could certainly be a guidebook supplement.
I thoroughly enjoyed The Lady and The Monk: Four Seasons in Kyoto by Pico Iyer. I'm not sure if someone who hasn't lived in Japan or come to know Japanese people really well would necessarily find it all that interesting though. As far as the discovery of the Japanese psyche and pointing out many of the cultural anomolies foreigners in Japan encounter, it's actually somewhat similar to Gaijin! Gaijin! except that it is written in a more sophisticated prose.
As far as guidebooks and the like go, I have read:
Kodansha Tokyo Subway Guide (I used this one only once as I found the Tokyo City Atlas, below, to be far more useful and comprehensive.)
Frommer's Japan (Frommer's doesn't have a Kyoto only version so I cut out the Kyoto piece for something light and small to carry around while in Kyoto and the surrounding areas. Click on the link for my full review.)
Little Adventures in Tokyo: 39 Thrills for the Urban Explorer (I didn't have time to really do the things this book suggests. It is well written, and I would highly recommend it to someone living in the Tokyo area or who will be in the Tokyo area for a week or more.)
Japan: Eyewitness Travel Guides (I really liked the Italy version of this on my trip to Italy in 2005. For Japan this was more interesting and fun to read than Frommer's. The book is heavy though and doesn't cover enough. There should be a different Eyewitness Travel Guide for each prefecture instead of one for the whole country. Then it could be lighter and include much more information.)
Tokyo City Atlas (This book is a must have if you are going it alone in Tokyo.)
1,000 Places to See Before You Die: A Traveler's Life List (An overly hyped book that won't be going to Japan with me. It may be OK to read at home to get an idea of places you may like to visit someday. But the details are scant, and none of the places to see are hidden discoveries. They are all places people have probably already heard about. Don't take this book on a trip with you. Get something much more specific to the country or place you are going to.)
Kyoto: Seven Paths to The Heart of The City (Beautiful book--I wish I had time to do all seven of the paths. We only had time to take two of the seven and they were both fabulous. The maps weren't that great or easy to follow. We would have totally missed these two wonderful paths had we only relied on Frommer's Japan.)
Exchanging US dollars into yen before or during your trip to Japan
Pictures from Japan
Where to stay in Japan
Professional Japanese Baseball
More things to read on Japan and learning Japanese resources