Travelocity - be sure to use the Fare Watcher section to track any changes to prices of flights---it will automatically send you an email letting you know when the price of a flight changes

Orbitz

Expedia

Priceline - this site lets you enter a price that you are willing to pay for airfare, hotels, and rental cars.  It has agreements with all the major players although you are not usually allowed to accrue any frequent flyer miles since you can get some great deals (i.e. published airfare is $200 and you bid $100 and an airline accepts the bid).  You don't even have to wait until the last minute to use Priceline---it accepts bids for future travel as well as last minute travel