There once was a tool called Active Work Tracker for Windows from Brigsoft.
What it basically did was to monitor user activity, sound alarm after a predefined period (say 60 minutes), wait another predefined time (say 5 minutes) when user was supposed to take a break (which was recognized as lack of activity), and repeat the whole procedure.
In addition, it recorded the total time user spends on his computer and presented nice charts.
I wonder whether there is a similar application for Ubuntu?
You can see more detailed description of Active Work Tracker at http://www.abstime.com/bsactivity/