However, I recently started using hipmunk. I remember hearing about it on This Week in Startups and Founders Stories.
It works great. There is something about the UI/User Experience that is beautiful and calming.
The concept of scoring based on agony (combination of price, duration and number of stops) is awesome, as is the automatic hiding of "worse" flights.
It's close to the experience of asking a personal assistant to book a flight, and having them make smart decisions on your behalf.
I remember thinking about how business travel should work:
Tell the system where you need to be and when (eg actual meeting locations), and have the system optimize flights, taxis, trains, hotels, buses, rental cars, visas
This should be the next step for Hipmunk