M.C.
On any given day, you will find similar fares on different sites. The trick is that fares vary A LOT day to day.
I start on kayak.com. They'll give you a 30-day graph of airfares, so you know if they're currently high for a given route. You can also sign up for notices on a given route--I get an email anytime roundtrip Dallas-Boston (where my sister lives) is under $250. Which happens more often than you'd think--I got $198 over Christmas! Once you find a good deal, however, I would agree with the post below that things usually go best if you book directly with the airline--use kayak to see, for example, that United is cheapest, then go to the United site to book the fare.
You can also check out farecaster.com--this will give you probabilites on whether flight prices will go up or down. Be patient and flexible, and you can find a good deal!