I used to love Kayak to search for airfare, it still works for me but I prefer the functionality I get with the ITA Matrix program. The ITA program allows me to enter all the airports I am wiling to use, not limited to four like on Kayak. There are often five or six airports I am willing to drive to if the price is right, I can search them all at the same time on the matrix.
On the first screen enter your airports, trip length and other options. If you take some time you can search by airline code also.
Screen two shows you the dates with the cheapest flights based on your calendar dates and trip length.
Click on the starting date you wish to book or learn more about and screen three opens to the flight information.
Unlike Kayak tickets cannot be purchased by a direct link, print out the flight times you desire and book them directly on the airline you are flying with.