I like to use kayak, expedia, google flights or the itamatrix to find my flight and airline of choice, and then book directly on that airlines's website. That way if there are problems there is no third party to muddle or slow down resolution. Some of the smaller and apparently cheaper online travel sites have terrible reviews and nasty horror stories.

My upcoming trip was booked on AirCanada.com, though I had expected Icelandair to be the better (cheaper) choice in the early days of searching. Last trip was AirFrance.ca