Agents offering cheap flight searches
These companies get a small percentage from the airline for bringing them new customers (just like traditional travel agents) but they are more streamline opperations with lower overheads which means they can generally offer better flight bargains to people like you and me.

Skyscanner. These guys have a great night and have invested a lot into fast database queries. Whether they are always the cheapest option is a matter of debate.

Expdia have proven to be first class agents with a great reputation for finding the deals. I am inclined to recommend Expedia for most highly traffic flights. If you are off to less well-known destinations they may not be quite as good.

Alternatively go directly to the airlines