I've used kayak, expedia, and various airline flight websites directly (eg, jetblue / southwest are the "discount" airlines".
America west you can book through expedia or go direct and save the $5 booking fee that expedia charges.
However, if you're ordering a package deal, then expedia will tend to have the best overall price....
If you buy any plane ticket make sure you look at the days you want to travel. Wednesdays seem to be the least expensive day to travel for me.
is the best website to buy plane tickets at a cheap price.