I've just ordered some parts for this project and, while waiting for the postman, I started prototyping with stuff laying around in my parts bin. I'm using a yellow LED in lack of a vibrating motor.

It's still early in the process but at least there's some rudimentary functionality there. You can push a button to start a Pomodoro and after five seconds the LED will fade in and out for some time alerting you that the Pomodoro has ended. The finished product will alert you with haptic feedback instead of a blinking LED and, of course, the Pomodoro will last for 25 minutes.

I'm using the Arduino Uno for prototyping but will probably settle for "vanilla AVR" later in the project. You'll find source code and breadboard layout on GitHub.