There are a few great sites suggested here, especially http://www.tripeedo.com and http://www.whichbudget.com for airfare search. But I wish the entire last paragraph wasn't an advertisement for a scammy, pay-for-advice frequent flier site.
I've found www.skyscanner.net quite good too, especially if you have a flexible schedule, as it lets you choose a whole month and shows you which days have the lowest lowest fares.
