Travel websites include those without booking fees such as CheapTickets and Expedia. There are also some that require you to bid on flights such as Priceline.com.
Most airlines offer flights even cheaper than the travel websites. Use a site such as CheapTickets for the convenience of comparing airlines, then go directly to the airline website and check the price there.
Travel agents have access to a database that's more complete than any online source. They have information on regional carriers as well as current promotions and deals.
Every travel website and travel agent charges less for flights during off-peak flying times. This is roughly from noon Mondays to noon Thursdays, as well as Saturdays.
Book two, if not three, weeks ahead for the cheapest airfare tickets. Go for a month in advance on international flights. The price goes up as the travel date nears.
Book at nearby airports for the cheapest airfare. Sometimes driving an hour will save you hundreds.