Many consumers assume that their favorite airfare booking engine or "aggregator" includes fares on all airlines. This simply ain't so. Airfarewatchdog researchers have found that some sites exclude certain airlines, either because these airlines only sell seats on their own site, or sometimes because the airline refuses to pay the aggregator or online travel agency (OTA) a fee for listing its fares. And this can change over time. A site may list an airline temporarily in order to demonstrate the financial consequences of being delisted, but usually the banished airline won't budge anyway. (JetBlue's fares seem to come and go on Orbitz, for instance.)
Or an airline may add or remove its fares owing to a dispute over commissions. A couple of years ago, United's fares mysteriously disappeared from Travelocity for several weeks. We suspect but cannot prove that this was a commission spat. Travelocity did not offer an explanation as to why this happened. And we wouldn't be surprised to see Virgin America's fares popping up on more sites in the future as the new carrier gains traction.
As an interesting side note, Kayak has been playing a cat and mouse game with Southwest over the last few months. Their flights, but not fares, will pop up briefly and then disappear in a flash when doing a search from, say, Baltimore to Ft. Lauderdale, a route that Southwest services. You'll see an "info" icon but no prices or other information. (Southwest explicitly prohibits using their Web site to mechanically "scrape" or monitor fare or other information.)
Here's a partial list of airlines that are excluded from the fare listings of various online airfare booking sites. If you discover others, let us know.
Orbitz: Sun Country, Jet Blue, Southwest, SkyBus, Allegiant, USA3000
Travelocity: Southwest, SkyBus, Allegiant, Virgin America
Kayak: Southwest, SkyBus, Allegiant, USA3000
Expedia: Southwest, SkyBus, Allegiant, Virgin America, Spirit, USA3000
Sidestep: Southwest, SkyBus, Allegiant, Virgin America, USA3000
In addition to this list, it's important to note that many international, and some domestic, airlines reserve their best fares for their own web sites, even if they do list most of their fares with a third party site. For example, even though Spirit lists its fares with Expedia, you won't find its 1 cent, 2 cent, and $1 fares listed anywhere but on Spirit's site. Alaska Airlines lists with virtually all OTAs, but has frequent 20% off sales that you'll find only on their site. Speaking of which, you won't find this 25% off sale to the Caribbean anywhere but on American's site. Check it out. For winter travel.