Looking for the best airfare? One of my favorite starting places is ITA Software (http://beta.itasoftware.com). They wrote the Orbitz booking engine.
This site is where they try new ideas. You know it’s unbiased since they don’t sell any tickets, just display the fares.
Check out their help pages. They have a “route language” that lets you specify all sorts of things (like connecting through a certain city on a certain airline).
And they have a monthly fare display. Say you need to go to Toledo sometime in February for 3 days, but you can be flexible when. They will show a calendar of the lowest fare each day. I’ve seen differences of 200% by changing a date by one day.
I then go to the airline Web site to book (and get the booking bonuses).