SideStep - Start here! This "meta-site" searches all the airline and online booking sites listed below, and displays all fares that meet your search criteria. When you find a fare you like, you get taken directly to the supplier to finish your booking. This helps avoid booking fees and allows you to use/accumulate bonus points and frequent flyer miles.

Other good online booking sites include:
Expedia
Travelocity
Orbitz
Hotwire
Priceline - Bid for travel
Mobissimo - Search international fares
ITAsoftware - Another "meta-site" that searches fares between any worldwide city. Log in as a Guest.

More online booking resources:
BiddingforTravel - Tips for effective bidding on Priceline
Seatguru.com - Find out the best and worst seats on any given airplane!
JohnnyJet - Lists the toll-free numbers for all airlines