A big sorry for the Windows users, but this app is for the Mac platform. I can only imagine that there are other programs for the windows and others. Time Out by Dejal is donation based so there really is no excuse for at least trying it out.
You can set full breaks at any increment (personally I am at 90 minutes with 10 minute breaks) and mini-breaks that help keep your eyes healthy (my personal preference is every 15 minutes to break for 10 seconds). It simply allows your eyes to adjust before you go back into work again. The app slowly grays out your screen (the rate at which can be set) which allows you to finish your thought before you go into the break...well thought out and awesome user experience.
There is also options to delay breaks which is nice if I am really invested in a solution that is close to being finished! So just a heads up for all the Drupal community to check it out.

Comments
Break Reminders for Windows & Linux: Workrave (opensource)
Check out http://workrave.org
It's free, open source, highly configurable, and works great! For Ubuntu users, you can find it in the Ubuntu repositories.
Sorry Mac users ;)
Thanks!
Thanks for the Time Out mention! I appreciate it.
By the way, the Dejal website is powered by Drupal.