1. The ideal time to fly is around 10 am. Usually delays pile up throughout the day, so the earlier you fly, the less likely you are to suffer delays. The very early flights are popular with people who want to get a full day in, so the midmorning flights tend to be the most civilized.
2. Always check the OAG before booking to see what flights are available. The OAG includes JetBlue and Southwest flights which the online travel agencies can't show you.
3. Make sure you're never on the last flight of the day if you really need to get somewhere on schedule. If something happens to the last flight, you're in trouble. As a general principle, while planning for this trip, I always checked that there was at least one alternative flight that would get me to my next destination on time. Since we fly first class at Fog Creek, if one of our flights got cancelled, the airline will work hard to reaccomodate us while the coach passengers might have to wait forever for a rebooking.
4. Fly out of smaller airports whenever possible. My favorite alternative airports: John Wayne or Burbank instead of LAX, Ft. Lauderdale instead of Miami, Love instead of DFW.
5. If the flight you're booked on is cancelled, don't wait in line with the crowds for the single, overworked airline representative. Get on the phone to your airline's frequent flyer priority number. They can rebook you just as well.
6. The American Express Platinum card pays for itself just from the free membership in Continental, Northwest, and Delta's lounges... not only because the lounges are quiet and pleasant, but because the lounges have unharried and experienced airline agents who are happy to help you with complicated problems, rebookings, and upgrades.
7. Final trick: never schedule an important flight during the last few days of the month, especially on Northwest. Pilots are only allowed to fly a certain number of hours per calendar month and by the end of the month they're running out of hours, especially on the more awfully-managed airlines like Northwest, so flights galore get cancelled in the last few days of every calendar month.