These are the flight consolidators that I first begin searching for cheap flights on. This list is by no means exhaustive, but these are the ones I tend to find the best prices on.
ITA software - doesn't directly sell flights, but a good source to find cheap routes.
KAYAK - the big daddy of flight search. Many websites are using Kayak for the back end and only put a pretty face on Kayak results.
My Air Deals - Not a normal flight search, but connects to special sales from major airlines.
Momondo.com - A decent search site, mainly distinguished by the graphs of when flights are cheapest.
Skyscanner - Primarily focused on the European market, can be useful for trying to use exchange rates to get a better deal by changing your location.... and dealing with the language.
Hipmunk - Hipmunk tries to rate flights based on "agony", this can be a good indicator of when it's better to go ahead and pay 10 or 20 extra dollars and not have an extra stop.
Flightfox - Not a flight search site per se, but a sight which allows you to post where you want to fly and let others do the searching. Read my overview of the service and my experience posting a flight part 1 and the results in part 2.
The Budget Airlines - this shows the budget airlines flying between two airports and is quickly becoming one of the first tools I go to.