I'm a big fan of Pomodoro, and from the looks of your default timer settings, so are you. I use a lot of macros when my timer session begins and ends, and there are a couple of ways I can see this happening in Freeter.
Run Command on Start/Stop
Probably one of the easier ways to accomplish this would be to have the ability to run a command on start/stop of a timer.
Keyboard Shortcut for Timer Start
Another somewhat easy way to do this I think would be to provide a keyboard shortcut selector for timers that I can use with Keyboard Maestro or similar to allow the timer to be started from macro applications.