When to book tickets from travel sites rather than airline sites?

Although they accomplish the same purpose for the end user, travel websites have different 'structures'. Kayak and SkyScanner for instance are 'travel search engines' - they simply search multiple airline websites, hotel sites, other online travel agents etc and then present the results. You'll notice that once you click on a result, you will be redirected to another website to complete the booking.

Expedia, Orbitz, Travelocity etc are all 'online travel agencies' - they function like real-world travel agencies in the sense that they file travel itineraries with airlines in the same way travel agent booking partners do. This means you can call / contact these sites for support, and often - depending on the airline - the only way to make changes is through the travel agent. On some international airlines, booking through an online travel agent means you won't be able to use web check-in facilities. etc.

The advantage of online travel agent sites is that they can negotiate cheaper fares with specific airlines directly - offers that you find elsewhere. This is particularly useful in certain verticals. For instance, STA Travel, an online/offline travel agent aimed at students - while fairly expensive for most other things - offers very discounted rates with select airlines; I've been able to get cheaper rates even when booking close to flight departure date. Similarly, many of the other bigger online travel agents also negotiate rates at times that can be better than what the airline's own website offers. Essentially, this is the problem search engines like Kayak are trying to solve by aggregating prices from different sources.

The catch is that because online travel agencies need to negotiate tie-ups with airlines, you may not find all existing flights on their site if they don't partner with that airline; this is especially true for international travel. Using a travel search engine thus usually gives a broader range of results, but keep in mind that many budget airlines often accept bookings exclusively through their own website and won't even show up on Kayak or Expedia. So it's always useful to search up a list of low-cost airlines operating in the region you're flying to and checking their websites individually.

View from developer side

Many (even not all) air companies that are providing the ticket search on their sites are using one of the major reservation systems (Amadeus, for example). This is because it far too easy to make a deal between company and search system over than hundreds of websites providing searching feature (which they get from the reservation systems).

The difference arise then user wants to but a ticket. In this case search site are still using the RS-engine, while air-company site uses its own way to book tickets. In many cases there is no huge difference between prices - search systems add some commission for their places, and that’s all.

The main point is that search systems and air-companies has various places for each flight (say, 20 places for sale by the Amadeus, and 10 for sell from company site). And in this point you can't say for certain, are places available or not.

As for usual, travel sites and Amadeus gets a huge part of places, and there is more chances to buy ticket from them, but from local sites of air-companies you can get some of special prices. Also there is charter flights, which are hardly available on Amadeus, and they are available only for local air-companies sites.

Airlines do very often offer better prices to agents and this surely includes online agents.

Plus some agents will lower their profit margins and sell cheaper than the recommended price that the airline will use to sell direct. Internet-only agents have lower overheads than storefront agents so can potentially offer bigger discounts.

Some airlines may reserve some special offers to only sell directly but I can't confirm this either way.

But websites often have extra booking charges on top of the ticket price so it can go both ways!

Most websites I've used won't give the full price including fees and taxes until you go right through the booking process.

Most of the online agents I've used that compare prices of many airlines (caveat: I've only done this in Australia) do not in fact include all airlines. (I'm currently on a trip with Korean Air which was not listed at all on Australia's biggest comparison site, Webjet, and was several hundred dollars cheaper than anything they listed).

My advice if you really want to find the very best price is to try multiple comparison sites and multiple airline sites directly and go right through the booking process stopping before processing your credit card or as soon as the site informs you of the true full price.

Write down each of the best prices and then take these to any agents that offer to beat any price. (I saved almost $50 more off my Korean Air flight this way)

Big advantage of travel sites is that they can show you flights for all airlines, not just one airline.

Hipmunk has taken the only sensible approach to displaying flights ("only sensible" to my eye, anyway). It presents a day's flight schedule as a chart, sortable by price, duration, arrival time, departure time, and "agony".

Once I know which flight I want, I check prices and availability across the travel and airline websites. I don't recall that I've ever uncovered huge price differences but sometimes seats are available on one site and not another.