I've also had ongoing problems with my eustachian tubes. I've used several methods to avoid discomfort:

1. 30 minutes before takeoff, use Afrin nasal spray (or something similar). Right before takeoff, use the spray again. My ENT explained that the first time you use it will open it up, and the second time it will be able to get in even further. I know the stuff is addictive, and this is the only time I use it.

2. I always have a large bottle of water and find that drinking it is more effective for clearing my ears than the regular things people do (simply swallowing, holding nose and breathing out, opening mouth and wiggling jaw).

3. Sudafed/decongestant before takeoff (and if a very long flight, before landing, too).

4. In extreme situations where you can't unblock your ears and you're in pain - ask the flight attendant to bring you a styrofoam/paper cup with a scalding hot damp paper towel in the bottom. Hold the cup up to your ear against your head, and sometimes this will help loosen things.

Ultimately, my eustachian tube problems didn't end until I had sinus surgery. I haven't had a problem since.