Does just what you want. I've tried a few of the more complex apps and this is a really good implementation of the essential functionality. Nice clean design as well.

One piece of feedback from trialling this morning - when the timer went off, the settings window popped up into focus. The timer options (where you set 25 minutes, etc) was active and I was already typing. This meant that I could have messed up the settings.

Consider whether are more general pop-up message would be better, or perhaps provide the user with the option of turning this on/off.

Great job overall.