Book Air
Be sure to check on the individual airline sites as you may be surprised to find that the prices are the same or better than what you find elsewhere.
Some airlines, Southwest for example, don’t show up in many of the search engines.
An excellent resource, that doesn’t offer booking capabilities, but does show fares is ITA. Follow their instructions about copying the itinerary and contacting a travel agent who can book these fares for you.
Be sure to look at the Book All Travel page for more options.
Here are some other air-only travel booking engines:
Air France – Click here for the lowest available Air France fares.
Cheapo Air – Save on domestic & international airline tickets. 
Condor – Get to any European City in a heartbeat! 
Economy Travel – In addition to international airfare, Economy Travel also has rates for missionary travel.
Fare Compare – As its name suggests, Fare Compare searches multiple sites to find the best fare.
Skyscanner – Skyscanner also has a hotel search function.
Sky Tours – Compare flights at Sky-Tours
Travel Team – The Travel Team seems to specialize in the South Pacific although they do also have Europe booking possibilities. Check them for tours and cruises as well.
Volaris – A budget airline with flights to Mexico from LA and San Francisco
Wegolo – Compare flights at this site
, which supposedly includes budget airlines in its comparisons.
Whichbudget – Whichbudget offers airfares on 136 airlines in 145 countries.