I always book our own travel and I've collected a few sites that I use. Most of the sites here I have personally used. A few are recommended by the Frugal Traveler Blog. I am quoted in Chris Elliott's article on fall travel deals.
Kayak
A great site for searching for flights. I absolutely love the side filters and their iPhone/iPad app.
Hipmunk
A very cool way of searching for flights. The interface is probably the best view of flights. Its Gantt Chart like display is intuitive and allows the user to quickly and easily see all of the available flights.
iPhone/iPad app
Southwest
Southwest doesn't allow other sites to index their site, so you have to go to southwest.com on your own.
iPhone app
Google Flights
Clean typical Google interface. For the destination, broad terms, like Europe, can be entered.
Rome2Rio
How to get from point A to point B. It can combine bus, train, and, air into one trip. Very clean interface. So far, I've just played with a little.
Momondo
Another meta-search engine like Kayak. Momondo does seem to have better low-cost European coverage than Kayak.
RouteHappy
RouteHappy assigns a Happiness rating to all flights. The Hapiness rating is a combination of amenities. It is quick view of information that is usually spread over many sites. In addition to the airline generated information, user reviews are also used. Great interface and use case.
iPhone app
Bing Travel
Bing Travel uses historical data to predict if the price of a flight will change. It is fairly accurate. I check it if I am on the fence about buying.
Vayama
Vayama specializes in international flights.
wegolol
wegolol is a meta-search engine for low cost European carriers
Seat Expert
Is easier to use than Seat Guru; it allows you to search by your flight. It takes the guessing work out of the equation. Seat Guru seems to have more information, but I check Seat Expert first.
Seat Guru
Has a a detail layout of practically every plane (maybe all) used today. It has lots of great information.
yapta
Tracks price changes for flights and hotels. They claim to be able to get refund vouchers.
World Airport Codes
Comprehensive list of airport codes. Decent interface. I don't see any point in paying $1.99 for their app; I'll just use the site.
IATA - Personalised Passport
IATA's site for passport, visa, and health documentation for any country.
List of Baggage Fees
airfarewatchdog's comprehensive list of baggage fees
Great Circle Mapper
Great Circle Mapper will map the number of miles between one or more airports (or one or more itenaries). PIT-CDG will show the distance between Pittsburgh International Airport and Charles de Gaulle. Read the FAQ for more instructions.
flightradar24.com
Very cool interactive map of all the flights currently in the air. Click on a plane to get more information.
Hipmunk
Hipmunk's hotel search is now one of the best, maybe the best. Its heat chart capability is awesome.
Kayak
A great site for searching for hotels too.
rocketmiles.com
Books hotels and for each booking they award airline miles. The miles vary by hotel and city. T he offer limited hotels in each city, but the number of miles awarded is better than pointshound.com.
Resort Fees Checker
Check for resort fees by city or hotel.
TripIt
Online free service that keeps all of the your itinerary in one convenient place. TripIt integrates with GMail, so you no longer have to forward emails. TripIt will automatically detect new travel related emails in your GMail inbox. TripIt is one of the best websites and iPhone/iPad app, highly recommended.
TravelMuse
TravelMuse bills itself as a travel planning organizer. The site mostly works, but I have run into some small snags. TravelMuse allows you to save your travel information in a single place. It is an improvement over my use of Google Bookmarks.
Trip Advisor
Trip Advisor has lots of reviews. A good place to start when looking to plan a trip. I use Trip Advisor for all kinds of information.
iPhone/iPad app
WikiTravel
Like its cousin Wikipedia, WikiTravel has tons of information. Highly recommended, lots of useful information, e.g. a nice article on European discount airlines.
World Taxi Meter
World Taxi Meter estimates the cost of taxi in many cities.
Rick Steves
Rick's books are well written and comprehensive. Excellent attention to detail.
Luxe City Guide
Nice comprehensive city guides.
Nile Guide
Nice comprehensive city guides.
Virtual Tourist
Nice comprehensive city guides.
Flight 001 Travel Store
Sells all kinds of travel related gear
Elliott.org
Christopher Elliott's very informative blog.
Frugal Traveler Blog
Great travel blog.
My Cruise Recommendations
Tips and cruise related websites