Airfare
This site does an excellent job searching multiple sites for the lowest airfare. You don't book with them, but they do link to the proper site.
A consolidator that often has excellent fares to Europe.
With all the budget airlines now flying within Europe, figuring our which airline flies where can be confusing. This site lets you pick your starting point and destination and tells you which airlines fly that route.
Europe
A booking site for european hotels.
Usually has the best deals for car rentals in Europe.
The draw here is a feature that allows you to enter a Paris address and see an actual photo of the building and street. Curious about the location of a hotel or apartment? This site can tell you.
Japan
If you want to book a traditional inn in Japan it can be a bit daunting, as many inns do not have english websites. Japanese Guest Houses has many options to choose from, and they handle the booking.
This site lets you enter your starting point and destination and tells you what trains you can take and how long the trip will be.
This is the japanese government's official site with plenty of helpful tips for planning your trip.
This site gives you information about the different passes and prices, as well as where you can buy them.
Travel Planning
The best part of this website is the forums, particularly Europe, Asia and US.
This is the site to visit for information on anything airline related, from frequent flyer programs to sales to mileage runs.
This site gives good information on any airfare/hotel deals going on. You can subscribe to their weekly top ten list.
Probably the most comprehensive site for hotel reviews, though its popularity means you need to careful of false reviews.
A must if you are considering bidding for a hotel on Priceline.com. Learn the tricks for bidding and how much to bid. If you ask a question, though, be sure you've done your research beforehand or prepare to be chastised.
An excellent resource for planning a European trip, including budget plans, reviews, and forums. The idea is to travel slow, spending at least a week in each place instead of rushing. Most helpful for Italy, but info on other countries is ever increasing.
Ever wonder what seat to pick when booking your flight? This site displays airplane layouts and tells you which seats are the best and which you should avoid.