Workrave is actually the program, Manfred has given me. The program basically records the user interactions with the program, by simply recording keyboard or mouse actions. Workrave distinguishes between "Micro-breaks", "Rest-breaks" and "daily limits". All of them are clearly fully customizable, so one can for instance define a micro-break every half an hour, rest-breaks every two hours and a daily limit of about 8 hours. Workrave runs quietly in the background and when the corresponding break happens, an information window pops up. Interestingly it doesn't only inform about the break but it additionally shows a cyber-girl (no, not in that sense :D ) doing exercises that should help you relax. In my opinion, however, these exercises shouldn't be performed AGAIN in front of the screen but it is much better to stand up and have a little walk in your room, ideally by going somewhere on the balcony and get some fresh air.
Here you can see some screenshots in case you may be interested. Moreover since the program uses the GTK runtime environment it runs on Windows as well as on UNIX systems.