I use kayak a lot. I also use bing, which used to be--I think--farecast? I like that they have a fare predictor, which will tell you how confident they are in advising you to wait or buy.
Since Southwest doesn't participate with kayak, I go straight to their website to check their flights. Last but not least, we're actually using Allegiant Air to fly non-stop from Hagerstown, MD to Sanford, so I check their site too!