If you're not familiar with Kayak.com, you're probably paying too much for airfare. The site is an online aggregator of content from sites like Expedia, Orbitz, Travelocity, JetBlue, United, Alaska and thousands more (they also do hotels and rental cars). You input your desired information and they spit back a list compiled from all these many sources.
I see this type of vertical search as a great way around travel agent sites like Expedia (which I like and use). The airlines would all rather offer better prices on their own sites, so web users will visit them directly instead of the agent sites. Likewise, consumers would rather buy directly from the airlines, as they'll get all the accompanying percs (miles, upgrades, seat selection, etc.) that aren't always available through the agent sites. Kayak is a brilliant example of a free aggregator and I think vertical searches are destined to follow this model.
The question that remains will be how companies like Expedia and Travelocity will respond to this threat. With no good reason to visit their sites (unless they block Kayak's spider and manage to get better deals than the direct airline sites), you might suspect that their days are numbered.
I think that flight companies, as well as many other merchants should focus on their site's purchase experience and produce landing pages that convert.
Price comparison has become a valid phase in many web-based product researches and as long as the aggregators generate leads - the pill is sweetened and most of the players are happy.
Related - a recent interview with Kayak's CEO Steve Hafner from Comparison-Engines.