Here are some of my favourite websites, organized by category.
Consistently found to have the cheapest flight options. I suggest start with a broader search engine to narrow your search and before booking always plug in your choice into Orbitz to make sure you are getting the best deal. The ability to search airports with a 80 mile radius is a bonus.
Great place to start a flight search when you are flexible with dates or even places. Although does not always give you a comprehensive result, does allow you to see some incredibly cheap options.
From the creator of Reddit comes an awesome travel planning site. I particularly like their “deals” section, where you can see upcoming deals from your city in the next few weeks.
I haven’t had a lot of opportunity to really try this one out yet, but its interactive map is an awesome way to see the flight options/costs all around the world from your hometown.