Where is the best place to find cheap flights?

I have been using Kayak for quite awhile, but I'm wondering if there is a good alternative I can use to make sure Kayak is still delivering cheap flight prices from all options.

I also heard that some airlines are taking their flight prices out of the large online sites.  Southwest has always been like this, but other airlines are doing the same thing.  Does this mean we will have to go back to the days when we needed to visit all of the sites of the airlines to compare prices?

Please help me find the best place to search for and find cheap flights.