Workrave (Linux and Windows)
Workrave is a freeware program that assists in the recovery and prevention of Repetitive Strain Injury (RSI). The program frequently alerts you to take micro-pauses, rest breaks and restricts you to your daily limit. Please refer to the feature comparison for a complete list of features, and how the program performs with respect to other programs on the market. The program runs on GNU/Linux and Microsoft Windows.
http://www.workrave.org/
AntiRSI (Mac OS X)
AntiRSI is a program for Mac OS X that helps prevent RSI (repetitive strain injury) and other computer related stress. It does so by forcing you to take regular breaks, yet without getting in the way. It also detects natural breaks so it won't force too many breaks on you.
More freeware programs:
GNU/Emacs type-break-mode, DrWright, OosTime, XWrits