Create a standalone timer app
Perhaps on Adobe Air? Just something that shows a dropdown of assigned tasks and allows you to start/stop the timer.
I'd like to help creating a browser extension for this, do you have a public API I can look at?
Ville-Kalle Arponen commented
If it would contain a pomodoro type of alarm and countdown, then it would be an even more desirable app. https://en.wikipedia.org/wiki/Pomodoro_Technique