Travel sites such as Cheap Tickets, Expedia, Orbitz and Travelocity allow you to display many of the flights between routes of a certain date. Not only can you sort on price and find the cheapest ticket, you can also sort by date to discover which days offer the least expensive options.
Airlines often boast that the cheapest tickets are available only on their website. After you determine the least expensive airlines through a travel site, go to the websites of those airlines, such as Southwest, JetBlue or Delta, to see if discounts are available with purchases directly from them.
Though travel agents may seem to be the most expensive options since they charge fees for their services, many have access to reservations systems not available to the general public. In addition, they may buy tickets in bulk to resell to customers at lower prices than the airlines. If you can't find a local agent, try Liberty Travel or STA Travel, or browse the members list of the American Society of Travel Agents.
With airlines cutting back on the number of routes and flights and charging extra for such previous freebies as checked luggage and blankets, the cost of domestic flights seems to spiral upwards. However, a little research can lessen the budget bite.