I looked at the Pomdoro site, and I'm intrigued. I don't understand something, though. How does it work with programming?
First of all, programming tasks defy time planning, as the next unplanned time-sinking bug or unforeseen difficulty always waits just around the corner.
Second, when you are in the zone, a timer going off every 25 minutes will just cause aggravation.
You can look at it as an agile process. You don't model your whole project at once, but when you start a Pomodoro you commit to working focused for 25 minutes. When the time is up you can prioritize differently or make a push on an unplanned item.
Also, I totally agree on your in-the-zone statement. I currently only use Pomodoro when I am having a slow day and I don't want to let the procrastination get the best of me. When I am in the zone I don't need Pomodoro to help me! =)
If you want to try it you should also check out my open source client, http://code.google.com/p/pomodairo/ =)