If you're working with a travel agent, indicate to them that you want the lowest fare possible. Just searching economy class won't always turn up the cheapest flight.
Contact budget airlines that specialize in no frills, low cost flights. Some examples include Spirit Air and Air Tran.
Consider flying on an off travel day. Flying in and out on a Tuesday, for example, will often turn up cheaper flights than on a weekend day.
Visit travel sites that compile flights based on price to see what carrier is running the cheapest flights for your route. Some examples include Expedia, Orbitz and Travelocity.
Try to fly with the same airline every time you travel. Certain airlines, like Delta, offer frequent flyer programs that you can use to earn free flights once you've accrued a certain number of miles.
Fly stand-by if your schedule allows you some flexibility. Stand-by means showing up at the airport and taking the next available flight out. Airlines fill empty seats at the last minute with Stand-by passengers. These tickets are often sold at highly discounted rates.