The previous respondent was right: The "best" airline will largely be determined by your specific needs.
Here's what I'd recommend: Rank order the following in terms of importance to you -- price, number of connections, and departure/arrival time. Think carefully about which of those three you value most, which you value the least . . . then drive your search based on those rankings.
Next, go to a good "roll-up" site that searches multpile booking sites for you. I recommend Kayak.com because they search all the usual suspects like Expedia, CheapoAir, and BookingBuddy; but also the airlines' own sites (Continental.com, etc.). In this way, they'll do all the work for you.
Once you've done your search, Kayak will let you modify your parameters: Want all the prices listed from lowest to highest? You can do it with the click of a mouse. Only want non-stop flights? Click and it's there for you. How about only departures that leave after 10 a.m.? One click does it.
Doing this will help you sift through an otherwise overwhelming amount of information. Play around with it for awhile . . . you might even find the search and booking process to be fun!
And no, I don't work for Kayak, I just love their site. It's what I use to book all of my personal travel.
These 3 are best for west coast USA flights, for price, ameneties, and service:
go to sites like spincitytravel.com. They list all the available flights in price order with number of stops. No airline is going to be better than any other for all things
If you ask 10 different people, you will get 5 or 6 different answers. Its all based on personal experience, frequent flyer program loyalty and other such things.
These days all the airlines compete with prices, so no airline is always going to be cheaper then the other. You might as well flip a coin to decide.