I fly weekly from Southern California to the Bay area. Nothing beats Southwest. Their on-time record is awesome, their rewards program is very generous (though they are starting to tighten up a bit), and they have many flights to choose from. Plus, they typically have room on any given flight, so if you get to the airport early you can simply jump on the next available. Flying from Southern Cal to the midwest, Expressjet is probably best. They have non-stop flights to Omaha for $200.
I recently flew Aeromexico and was pleasantly suprised. Nice plane, nice people, and free beverages. The only down side was that we had to listen to all the announcements twice, once in Spanish and again in English.
I absolutely hate United and will not fly them unless there is no other option. I've also had bad luck with American and Northwest.