Looking for an alternative to EyeDefender on Linux, I found this great program. It is free (Open Source) and quite configurable. I love how it is implemented - the breaks, the notifications, timers. The default values might require some tweaking, depending on your situation.
The default settings from EyeDefender are 2-minute break every 45 minutes. The settings I'm using are taken from the following link in a good article on ergonomic set up for the workplace - http://lifehacker.com/5755870/how-to-ergonomically-optimize-your-workspace
and they are:
Microbreak every 15 minutes for 30 seconds;
Rest break every 45 minutes for 3 minutes;
and a Daily limit of 8 hours.
WorkRave includes exercises that one can trigger manually. These automatically pop up during rest break. I really like the program so far.
Some related articles with comments on break time and frequency: