Travel guide Airport Explorer has an excellent site devoted to airfare deals. First, it steers you to airfare aggregators like Farecast, Kayak, and Yahoo Farechase, noting that they're "usually the best bets for cheap flights." Next you get links to discount search engines such as CheapTickets, Priceline, and Orbitz. Finally, the site directs you independent airlines like JetBlue and Southwest.
Obviously this isn't groundbreaking information, but it's all presented in a logical, well-organized way that makes for easy perusal of the various sites. The guide also provides info on using one-way flights to your advantage and booking multiple cities, along with answers to frequently asked flight questions. In short, it's a stellar resource for anyone looking for the lowest possible airfare. Check it out.