I have mentioned this company before, but it is worth mentioning again... check out The Flight Deal Daily and sign up for their newsletter to find the best flight deals if you are flexible about dates and locations. Just as an example, one of today's deals is on American Airlines from NYC to San Francisco, and costs $272 for a round trip flight. Not bad... especially if you want to come visit me!
What travel tool should you use to book your flight? My three favorites are Kayak, ITA Software's Matrix Airfare Search, and Hipmunk. Keep in mind, Southwest intentionally opts out of travel tool websites, so be sure to check directly on the Southwest webpage to compare fares.
As a side note, make sure you are always signed up for the frequent flier program for the airline you choose to fly. Even if you don't fly often, it is worth doing. Who knows, you might end up on an international flight with an affiliate of the airline, racking up enough points to score a free domestic trip. Right now I am sitting on enough points to take a free flight on Delta and a free on Southwest. Where should I go?