Currently, the pomodoro timer opens a window that steals the focus from the current application.
While this might be good to signal the break, it can also affect current work. Especially when working with graphic or engineering applications where a single command might take several minutes (e.g. using a polygon mask in a graphics program), this might jeopardize the work of the user, making the technique inefficient.

Therefore I'd like to suggest to implement an option where a system tray popup is shown instead. When the user clicks the pop up, the window to tag the break is shown (as it is now). Optionally, a sound could also be played to emphasize the break.