After
this experience, I would highly recommend
Midwest Airlines. Of course the massive downside is
the flight routes. They have hubs in Milwaukee, WI and Kansas City so no matter where you're headed you need to stop in one of those two cities, and many times you are not given a choice.
It's my airline of choice, but, of course, 9 out of 10 flights have us headed to my hometown in central WI so we'd have a layover in the Twin Cities, Chicago, Madison, or Milwaukee anyway.
Price wise most of the airlines are pretty competitive now, depending on your flexibility in traveling you might be able to check out a variety of airlines. If you can use an airline that has a hub at your departing airport it will probably give you the most options for flight times and the best service (more counters, more personnel and better trained personnel).
For example if you were in the Dallas, TX area and wanted to head to Minneapolis, MN and then off to Boston, MA you might want to look into a round trip between DFW and MSP on American and another between MSP and a Boston airport on Northwest. The big hassle here is going to be the return trip. If you don't want to spend any time in Minneapolis on the way back you'll have to allow for enough time on the return trip to claim your bags and re-check through security to catch your next flight (of course this goes away if you're traveling out of a carry-on bag only but for the length of trip you're talking I doubt you are.