Here are some ways I've found better deals on flights:
1. Look for flights on expedia, cheaptickets etc, then when you've found the lowest rate, go direct to the airline's website to see if they are advertising the same flight for less.
2. Compare low-cost carriers with major carriers that fly to your destination and consider looking at airports further away since the best fares may not be out of the airport closest to you. I live in Boston, but often fly out of Providence to get better rates.
3. Be flexible on dates--you can often get better rates if you fly on Saturdays or Mondays because those are less optimal flying days than say Friday and Sunday.