Momondo - Momondo has won numerous awards as best flight comparison site and is recommended by the fine people at CNN, the New York Times and the Daily Telegraph.
Kayak - you can search hundreds of travel sites at once
Expedia - you can book airline tickets, hotel reservations, car rentals, cruises, vacation packages and various attractions and services
Adioso - this website uses natural language, so you can type “London to Southeast Asia mid May for 3 weeks into the search box and Adioso suggests flights]
Hipmunk - this site ranks flights by “Agony”, taking inconvenience into account
Firefox - this website is a marketplace of genuine travel experts. They have an extraordinarily deep understanding of flights, hotels, and loyalty programs
AirTreks - create and book a custom itinerary for an around the world or multi-stop trip in just three simple steps
Booking Buddy - you can save some of the hassle out of searching the various travel sites for the best fare.
Airfare Watchdog - one of the few travel sites that let you search by departure city, for when you just want to get out of town for a few days and don't really care where you end up, as long as the airfare is cheap
Hotwire - the website offers cheap travel and last minute deals
Yapta - the downloadable plug-in tracks the prices of flights you're interested in, letting you know the best time to book