Go to the Source
Multi-airline booking sites tend to bill themselves as the be-all end-all in low fares. And sure, you may find a great deal there. But in reality, you're likely to find an even better deal if you go to the source.
Before you purchase a trip on a booking site, check the prices for the flights you want on the airline's own Web site. Eliminating the go-between saves the airline money, so you can often save, too -- and sometimes save hundreds if the airline is running a promo [sources: Rosenbloom, Airfare Watchdog].
Also noteworthy is what might be missing from those go-between sites: smaller, low-cost airlines. Southwest, for instance, won't come up anywhere except on the Southwest Web site, and Allegiant is often absent from multi-airline search sites, too [source: Airfare Watchdog].
Eliminating the middleman isn't the only motive behind the lower fares, though. Airlines love loyalty, and you can easily take advantage of this.