Sidestep is my fav choice for published fares. But I sometimes check out ITASoftware.com (these are the people that developed the engine that runs underneath Orbitz and a couple other sites). Unlike Orbitz and Travelocity, ITASoftware is completely unbiased and gives you better raw data... but it doesn't sell tickets, so you have to go to the airline site to buy if you find a better deal.

Hotwire is sometimes good for unpublished fares if you can be flexible and take whatever time they give you for flights in and out.

Occasionally you can still get insane deals on the name-your-own-price on Priceline.

And Southwest is my very favorite airline. If I have a choice, I will always fly Southwest, even if another airline is a few bucks cheaper.